Honestly, I think that just about every aspect of AG was fundamentally flawed in some fashion. And just because I feel like making a nice big list of a post, and because my typin' fingers are feelin' cold and itchy, y'all'd best strap yourselves in for a long one. (Or, far more likely, ignore it entirely. Whatever.) (I mean it though. It's long.) So:
--The Aqua/Magma subplot
Okay, nothing more really needs to be said here; I think we can all agree that it was a gigantic glob of wasted potential. Although, I remember at one point reading a post on GameFAQs on the subject. It joked that none of the show's writers ever managed to defeat Liza and Tate, so they never actually saw the in-game conclusion(s) to the subplot. And so they decided to just BS the whole thing no matter the cost so they could then exact their revenge on the psychic twins by giving Ash the absolute biggest actual Deus ex Machina victory the show's ever seen.
I mean of course that's not actually what went down over there in Moonland, but would it really surprise anyone?
--Max and Brock
Okay, let me first get it out that I never liked Max. He's...probably the only main cast member that I've actually kinda disliked. Now, I'm sure that one of the main reasons Max was brought in was to kinda experiment with a new dynamic. Y'know, little pre-trainer kid, kid brother to the lead girl, getting the opportunity to experience a bit of the outside world and study for his own eventual solo journey. Cool. That's what was supposed to happen, in theory, and hey, credit where it's due: we did see a bit of that brother-sister dynamic in action. In practice, however...
Well, being a pre-trainer meant that he couldn't actually have any pokemon of his own; no participation in the actual plots of most episodes for you, kiddo! Which in turn meant that episodes typically had to be tailor-made for him, to the near-exclusion of his fellow cast-mates getting any development at the same time (especially Brock). So, y'know, he felt like this big load, sort of an anchor dragging the other characters down by virtue of rarely ever being able to help himself out of dire situations and being thoroughly incapable of doing anything meaningful.
Speaking of which, it also meant that he had to share his potential screentime with Brock. Not just in terms of potential development episodes, either (which, let's face it, both of them could have easily gotten more of these--too bad the writers wanted to reach that magical 33% filler mark); Max being there pretty much meant that Brock's already meager role as combination Mr. Exposition/Battle Commentator was also split. Less character focus for everyone, hooray! And of course the whole series was pretty much a continuation of Brock's steady downward spiral into obscurity and out-of-focus-ness, but that can be said of pretty much every saga he's been a part of, so.
Point is, I think I would've liked the series a tad better if it had been just Max or just Brock (or, preferably, just someone other than Brock) filling the "third wheel" role. Both characters being the third wheel simultaneously simply left both of them criminally underdeveloped. (I mean, come on now. With how often we saw anyone on Brock's team, can anyone really say there'd be a noticeable difference?)
--Ash's quest
Okay, there were some things that were marked improvements over the previous series. In functioning as sort of a mentor to May, we did see an overall slightly more mature character, giving him the illusion of personal growth. We saw his team actually do things like evolve (hey remember back in Johto when both Misty and Brock got more evolutions than Ash did?), which made it seem like they were in a frequent state of development as well; this was helped by the fact that they were no longer shackled by the issue of keeping everything completely marketable, so they didn't need to all be generically cute anymore (more on that in May's section). And hell, I don't think anyone can dispute that the average battle was far better than the fare we'd grown accustomed to. Which is why I don't think the issues with Ash's quests are anything really to do with Ash himself.
First, rivals. This's probably the biggest black mark against the series: the fact that Ash simply did not have any. I mean, everyone knows that some manner of persistent conflict is preferable to no persistent conflict. Without it, Ash's character feels stagnant; even his pseudo-mentor role wasn't enough to carry his entire journey, and it felt as though his team was developing with no real set goal in mind for the writers.
On the subject of Morrison in particular, well, I wanted to like him. Really, I did. He could've been a really cool character who would leave his own perfectly unique mark on the series. I mean, look at him: rookie trainer, exceptional strength for being a rookie, highly competitive and makes friends easily...and has a tendency to choke when he has to face those friends in a serious setting. It could've made for some neat interactions and development, especially seeing Ash mentoring an actual trainer. So then why, why did we not see him until just before the last badge? As it was, it was like the writers were all "holy @%#$ we forgot to give our lead guy an actual rival so let's make this random one-off kid return" and shoehorned him in at the last second, which made his dramatic BAAAWW I CAN'T FIGHT MY FRIEND moment feel incredibly forced, sudden, and cheap. It was very disappointing because that sudden development meant not only that the battle was pretty much the weakest of that tournament--doubly so because Morrison was supposed to be Ash's "man to beat" a la Gary and Paul--but that all of the best battles in the arc were against one-shot characters. Talk about skewed priorities.
And then came the Battle Frontier. Like so many things, it sounds awesome in theory: a bunch of locations with unique and highly specialized challenges and obstacles that challenge the player and their pokemon in a manner other than straight-up single or double battles! Awesome, right? I mean, that's how it was done in the games, right? It'll be kind of like the Orange Islands saga! And, being fair, I'm fairly certain that the writers were kinda going for something like an extended take on the Orange Islands. Like how there were still no rivals for Ash, and how it was almost a completely new region they were exploring (I mean, how many Kanto locales did they actually visit, besides Pallet Town? Like, five?). Which would've been fine--if they'd kept the spirit of the Battle Frontier intact (and thus what made the Orange Islands saga memorable).
And I know I'm not the only person who was highly disappointed with how they handled the Battle Frontier facilities. I mean, yeah, it was utter foolishness to expect the writers to replicate those challenges in full; I didn't. I was kind of expecting at least a semblance of those challenges to remain, though, and for the facilities, Brains, and Symbols not to be turned into glorified Gyms, Gym Leaders, and Badges. As it was, only the Battle Factory even remotely resembled its in-game counterpart, and only then because the Gym Leader's Frontier Brain's Gym Leader's team wasn't set in stone. It was honestly very underwhelming, to say the least. (And it kind of was right around this time that I had to stop watching the show on account of college and not having a TV in my dorm, which may or may not affect my opinion in some way, I really don't know.)
--And finally, May's Contest arc
Actually, this was arguably the best-handled part of the series. It was something new and fresh (holy @#%$ the main girl's actually doing something), if nothing else. As rivals go, Harley's my all-time favorite by far, and as main rivals go, Drew is arguably the best, on account of both receiving actual meaningful character development more than three episodes before his departure and having regular on-screen battles, and against May, even.
But even then... well, I dunno, my memory may be a bit foggy, but I kinda feel that May's personal development was...kind of lacking. Like, she improved as a coordinator, and all that. But she didn't really seem to change all that much as a character in the long run; at least, I can't remember anything being done about her tendency to emulate Ash's battle style, rather than developing her own, until the tail end of the series.
And remember what I said about Ash's team no longer being completely shackled by generic cuteness and marketability? Well, it seems all of that just got shifted over to May. Aside from Beautifly and Blaziken, none of her seven team members evolved during her run, and they all fit the bill of "marketable" if not "cute"; it really is telling that, following her departure, she was suddenly allowed access to the not-as-cute Wartortle and the decidedly not-cute Venusaur (to say nothing of how Blaziken itself was basically a parting gift). Basically, where Ash's team felt like it was developing at a frequent rate, May's team felt like it was in a near-constant stasis. I mean, hell, even Dawn got Mamoswine!
And then there's the contests themselves. Okay, yeah, they looked really nice for the most part, but many of them were essentially given to her, and as such were plagued by an amount of BS that would make Kanto-era Ash squirm. Like, remember that one time Skitty took about half a dozen Hyper Beams and such without going down, and yet May's points were only disappearing bit by tiny bit despite the fact that she was being outmaneuvered at every turn? And how she then landed one successful Assist, and her opponent's points then dropped by about half? Remember those times May visibly flubbed her appeal performances (like the instance where Harley was conducting sabotage, making her appear to be performing especially poorly), and yet still made it into the battle rounds with no problems? And how, in DP, flubbing appeals like that would be grounds for disqualification? Or hell, remember that time her never-battled-before-in-its-life baby Squirtle learned Ice Beam (just in time to use it to defeat Harley yet again, in fact), and the only problem it had with it was too much recoil? And how, barely twenty episodes prior, Ash's very own actual Ice-type required assistance from a passing coordinator and evolution to even fire one off correctly? And I could probably go on if I felt so inclined.
Although...it's kinda weird. Even despite all of these glaring flaws, I still enjoyed the series. At least, I did back in 2003-6. I can't say how well I'd enjoy it now that several years have passed and everything has had time to settle. Perhaps it has something to do with how Hoenn is my favorite region and Gen 3 is just about my favorite generation; back then, I guess the new stuff and the stuff the writers did well were enough to offset the stuff they did poorly; just as an example, the gym battle with Juan is one of the highest points of the entire franchise for me, and certainly the best gym match we've seen. And in retrospect, even though DP did many things better on a technical level, I still think I prefer AG (at least, DP's the only series where I didn't watch most of it by choice rather than by necessity), which would make it my second favorite series after BW. And hell, with the way I tend to look at the past, even that may change sometime in the future.