The only real issue I've had with the pokemon games (not just the fourth gen) is the number of seemingly-'useless' electric pokemon in the early-to-mid game. Plusle, Minun, Pachirisu, basically. I understand that they're basically fillers, but I can't help but to think that just giving up the Pikachu or replacing 'em with some sorta fire type in the fourth gen would've been a better route to go. Other than that... Well, for me, I like the 4th gen overall. I don't even mind Bidoof (easy Atk EVs, after all) so much, though it does seem redundant when we've already got pokemon like Rattata, Sentret, and Zigzagoon. The same could be said about a bunch of the pokemon we got this generation.
I do have a few minor gripes: Many of the TMs are one-time deals, which really hurts. Or, in some cases, you either play the slot machines forever or even worse, shell out over 200,000 in-game money to buy yourself a new TM24 (or, in some cases, even more). It'd be good to have a TM seller that changes inventory every couple days or week or so. Maybe I haven't gotten to this point yet, but bulk-purchases of the drinks (fresh water, soda, and lemonade) would be useful as well.
Some evolutions (and a pre-evo), I'm not a fan of. That doesn't mean they don't have their place somehow... Lickylicky, Chingling, Tangrowth, and Probopass, basically. That's just my personal opinion, though I can at least see Chingling as okay. The creation stories are a bit annoying but it's alright- how are they gonna top this for Gen 5? Destruction stories? Creation of Pokemon type story?
Wifi is nice (but removing the trade requirements information for GTS in Platinum was a bad idea). One thing I'm tired of is the Electric gyms, it's time to toss something else in their place next time.
I've been playing since my original Pokemon Blue gave me a Mew (alpha releases were great back then). Played through pretty much all of the games, for that matter, on the GB Pocket, GBA, GBA SP, and now the DS Lite. Though I wouldn't touch the real original generation with a ten foot pole compared to the third gen, I think I'd happily play GSC again thanks to my fond memories of it. Generation 3 wasn't bad (I hated the text in Ruby and Sapphire, however), but Emerald fixed that and added a lot more to the game as well. The fourth gen, of which I now play Platinum, is a game that I must admit that I am thoroughly enjoying... even if I've only won one online battle against a friend (and it was a fluke, of course), it's just that and having fun.
What can I say? After ten years, I'm still enjoying the series.