When did Pokemon Die? It was stillborn.
Base>Rocket was not all that great. Haymaker was too dominant. Played without Haymaker, it's quite fun though, but Blastoise is a little too fast.
Gym needed to be broken down into it's own block over 4 sets with Base>Fossil gone atleast. Not much made an impact. Didn't help that Surge and Giovanni were terrible. Gym SHOULD have been 8 viable decks if made well, with mixes of same types(Brock/Giovanni, Erika/Koga). Rocket should have mixed with Dark. By itself, not a bad block. Again, select cards are too dominant.
Neo was just urgh. Thanks to the GS games themselves. 6 Steel and 6 Dark mons through the entire game gave birth to Darkness and Metal Energy, the abominations they are. Darkness and Metal should have been absorbed into other types until RS, where basic Darkness and Metal should have happened. Then there's Sneasel and Slowking. Urgh. Too good.
Not too familiar with the E series. Never was experienced them.
Come EX and the EX mons, I don't think the game was all that bad. Sure, the EX were an abomination of Marketing and far too rare, but the game was better as a game than it had ever been. Come Holon, I think it said a lot when Metanite ran no EX mons. If the EXs had been toned down to normal cards, or not existed, this could have been an example of how to do this TCG. It still is, just minus the EX Super Rares. This is the high point.
Come DP, DP had a decent start. DP is a great base. MT.. not bad. SW on? BRO-KEN. Broken until atleast HGSS. Most every set, something to ruin the game. With HGSS, DP-ARC should have been gone. I know, a set should have a long time of play, but HGSS was too obviously a base(read: Reboot) and SP is a problem. It's likely going to happen this year, and the game should get back to early DP atleast.
I do have to give HGSS something, Prime/LEGEND are fantastic mechanics. Primes are not too rare, while a little strong, not undefeatable, and generally pretty good. Everything LvX and EX should have been. While LEGEND fills the 'OMG, AS A COLLECTOR I WANTS IT/Sells packets' quota.
TL; DR?
Game has always had massive issues, it should strive to be like EX or HGSS eras, not Base or DP. Rotations should happen when needed for City/State/National atleast, not dictated by sales.