* Kanto: A lot of its flaws can be justified since it was the original series. The writers/animators were 'finding their footing', so to speak. Some of its 'flaws', such as Ash earning a bunch of badges in unconventional ways or the anticlimatic loss at the league with Charizard's disobedience (although both of these points highlighted his rookie faults), weren't ever repeated. Never seeing Pidgeot and Primeape again sucked.
* Orange Islands: Tracey was an unnecessary third wheel. Releasing Lapras.
* Johto: Wasted potential with the GS ball. Dull middle stretch. Obvious executive meddling and disagreements over the direction of the show led to things such as the Ash x Misty subplot built from Kanto/Orange Islands to fizzle away (though it did show up time to time). Misty and Brock could have had more individual focus. Cyndaquil didn't evolve, even though it put up so much work. Johto captures deserved some more glory at the league.
* Hoenn: Not the finest fillers, that's for sure. Team Rocket had clearly overstayed their welcome by this point. More could have been done with Team Aqua/Magma. League should have been 1 or 2 episodes longer, and Ash vs Tyson deserved to be the semifinal (why repeat another Top 8 finish).
* Battle Frontier: Expected more appearances from Misty and Tracey. Obvious writing decision to make Ash a momentary idiot so that Charizard gets screwed over and loses against Brandon, to create 'dramatic tension' of how Ash was going to win without his ace.
* DP:: Brock was an unnecessary third wheel. Team Rocket. Ash's team soon became the Chimchar/Infernape Show. Suicide Mountain killed Torterra. Ash x Dawn should have happened in second half of the series - everything was there for it. Dawn's rivals could have been more interesting. Ash v Trollbias should have been a two-parter, so that way Swellow wouldn't have gotten P.I.S.-screwed over.
* BW: One of the most tragic decisions was to "reset" Ash back to Kanto/Johto levels, in terms of both personality and as a trainer. At the same, trying to fit this "reset" Ash with continuity to previous series. BW could have been a good series if it was simply another protagonist instead of Ash. Iris tried to be a Misty clone, but not as endearing. TP vs TR being cancelled, and episode N TP being disappointing. Charizard's reappearance was utterly pointless, and the Charizard vs Reshiram tease never happened. Cameron might be the worst character in the anime's history, and for Ash to lose 4-6 and regressing back to the top 8 felt like a slap in the face from the writers. Way too much Oshawott, and a bunch of neglected others on Ash's team. DA! was terrible. Yeah, pretty much everything in Season 2 was an utter trainwreck.
* XY(&Z): Serena's goal was delayed for a year, when there was no reason for it. SatoSere's retconned introduction, and not going anywhere with it, especially from Ash's side, since the beginning. Clemont's goal and development fizzled away, and there was no Lumiose City villain arc before his gym - not to mention, he was one of the only gym leaders who felt like an underdog to Ash, who just styled upon him as if he was an E4. Leprechaun should never have become Ash's rival - or he should have showed up at the beginning of the series as a slightly less experienced trainer than Ash who wanted to catch up to him, not as a complete newbie who becomes a super rookie with a Cameron-esque death squad in like 50 episodes. Serena's rivals were also poor, and to call them "rivals" and not as fodder is being nice. Showcases became boring and a worse version of Contests. The league skipping over all the rounds leading up to the semifinals was disappointing, when all it would have needed is one extra episode full of clips showing his progress. One of the most disappointing things is the complete self-contained nature of XY, and its lack of continuity to OS-DP, even though XY Ash felt like a post-DP Ash.