From DreamWidth (imported recently from LiveJournal):
https://dmxrated.dreamwidth.org/418595.html#cutid1
1) The non-existence of a "Light" type, which would be the true/i] counter-element to Dark. I know "Psychic" is also directly counter to Dark, but Fire is counter to both Water and Ice. Especially egregious from Gen II onward, when Dark and Metal were introduced as types.
2) Worlds are centered around the player. For example, you can plant a berry anywhere, and no one can simply come around and take what you sow. (To be fair, though, it's only natural that the designers of these games are only thinking about how to make them fun for the players, rather than about realism.)
3) All four regions in Gens III and IV have the same first 50 TMs. Gen IV just stacks 42 more on top of the Gen III set. Gen V has all the same ones as Gen IV, plus more, although all the new ones mingle with the rest of them, instead of stacking further up. Not that that makes much of a difference...
4) In GSC, Love Balls work on same-gendered Pokemon instead of opposite-gendered ones like they're supposed to, due to a glitch. In HGSS, they only work on anything of the same species and opposite sex as you pit against, which only makes them nigh useless, meaning that the only real reason to collect Pink Apricorns is to make ApriJuice out of. [/i]
[Since found out that that's how they worked even in GSC.]
5) Pokemon cannot bring items with them when migrated b/w Gens IV and V. And why?
6) Because Gen V introduces a "new" set of TMs (which, like I said, is actually a renumbered set with new TMs fitted in). Like, couldn't the games just have blocked Pokemon carrying a TM disk like they do w/ those who know an HM?
7) On top of that, TMs in Gen V can now be used infinitely. If the dev team wanted to let players teach them as many times as desired, why wasn't this true since Gen I? Memory issue? Plus, this takes away from the games' challenge.
8) All berry trees in HGSS now yield apricorns, instead of the Gen-III-equivalent berries to each berry variety that existed in GSC.
9) Everything just feels lifeless. Who cares that a downloadable or transferrable Pokemon knows some special move? Nothing has any real personality to it, characters or Pokemon.
10) The need to trade Pokemon for complete Pokedexes. Of course, these games are meant to encourage socialization among players, which is why they put out two or three versions of each game, but this does not mesh well with my personality as an autistic introvert who would rather keep things simple and orderly.
11) Some stuff only exists in the game code to obtain from external sources. (And yeah, I know, the reason for this is so that Nintendo can make side-deals with other businesses for mutual promotion.)
12) The fact that certain Legendary Pokemon are banned from all Battle Towers, Frontiers, and Subways, while others are permitted there. Even if the reason was to test your real skills as a Trainer, and because all players will have access to them (which is exactly what I'm talking about with #2), that would make more sense if all
legendaries were banned.
13) There are as many Pokemon with a 7/1 male/female ratio as there are equally-gendered ones, but none with a 1/7 M/F ratio.
14) I know inanimate objects can't reproduce in real life, but if a Geodude can do so, why shouldn't a Magnemite be able to? Not like rocks can fornicate and reproduce in real life either, and yet there's an egg group called "Mineral".
15) The ability to clone Pokemon (since day one).
16) Why can a lot of Pokemon only have one ability or the other? Biologically, they should have both.
17) The fact that e-Reader berries were very inconsistent in use, and you can only have one variety at a time.
18) Why are only certain "cute" Pokemon allowed in Amity Square, but not others like Togepi, Jirachi, or even Clefairy's pre-evolved form Cleffa? Add to that the fact that the Sinnoh starters are only allowed there in Platinum, in which their evolved forms also are. (Infernape? Cute? Yeah, sure...)
19) Certain "breedable" moves can only be known by bred Pokemon if the father is a given species in particular. No, it's not enough that the father simply knows the move in question, nor am I gonna bother naming examples. Just look up any Pokemon species or move on Bulbapedia, and you'll see what I'm talking about.
What really ended my relation with the games, was finding out from TV Tropes: The Computer is a Cheating Bastard, that the RNG is rigged against you in Trainer battles, particularly in the Battle Towers and Frontiers (the more of a winning streak you attain). Some say this isn't true, that there is no actual evidence of this in the game code, but I've seen others give testimony and even record video clips to point stuff out.