So I was told to come here to add my rant list so here goes :D
Gen 5 negatives
No genies in bw2 and dream radar is annoying to get and playthrough.
To many things require access to the other 3 game versions, like prankster genies, keys, entree and funfests and medal requierments.
Serious lack of wifi options in comparison to gen 4, most things like unova link, entralink and subway are wireless or infrared only making it extremely awkward to complete these features.
Multi subway is terribly designed, for one you cant link up with a friend via wifi to get the trophy and to make matters worse you only have 1 choice of AI to team up with who has a very mediocre selection of pokemon and you dont even get to see what they will be using beforehand so you cannot bring a team to synergize with them, making the challenge completely inconsistent and luck reliant, considering in gen 4 you had 5 AI choice partners with good legendaries and drastically better pokemon and could wait for them to have a team that synergizes with yours and even then it was hard, this gen took a huge step backwards in this area.
All kind of commemorative achievement things were removed like symbols for subway bosses ( gen 4 had trophies to for battle tower so we are not counting those ) stylish ribbons, and stars on trainer card, without looking up the colour upgrades there is no way to tell a trainer level by merely looking at the card.
Alot of medal requierments are ridiculous and add no challenge or fun to the game such as passing 1000 people or doing a funfest with 30 people, the medals idea was great to make you try everything the game has to offer but the final version of the product is not to great.
Musicals are contests with no actual substance or challenge and are utterly boring
Movies are better than musicals but still not that captivating they are way inferior to pokeathlon and gen 3 and 4 contests.
Hgss cons
No story in kanto which feels bit dry and empty they could have expanded the rocket giovanni and silver storyline into kanto.
Customisable safari was a fun idea but the final version of it is horrible, having to wait nearly a year for some pokemon is just insane what where they smoking at the time lol.
Repeat battle frontier from platinum feels a bit cheap, could have at least brought back emerald frontier instead which was awhile ago and would have felt fresher in a gen 4 game.
Gym leader numbers are way to awkward to get without online research which you should not need to resort to, way it worked in emerald and platinum was fine.
Platinum cons.
Id say the game basically has none except for a few not massively important things like some gen 1 and 2 pokemon sprites instead of changing them they just made them get stuck like mid animation the result looks bizzare like a cut off gengar and a raichu and geodude that look like they need a shit lol.
And since alot of pokemon moved into the sinnoh dex many routes were left without a radar exclusive pokemon or a swarm pokemon so they could have taken some pokemon that are gba cart exclusives and made them into radar exclusive or swarms reducing the need for so many gba carts to get or chain every pokemon, and on this topic in south route 204 ralts is no longer a radar exclusive so they could have made sunkern be the one for the whole route rather than just the north part where its impossible to chain it because there is not enough grass.
Emerald cons
No second improved league like FRLG makes it a bore and very hard to level grind and on top of that you can only battle Steven once in the whole game rather than once in awhile at least like the gym leaders, and there is no postgame area with decent level trainers to level grind so its a mercy you can clone in emerald otherwise leveling stuff for the frontier would be a nightmare.
Not being able to battle the rival later in the game sucks, they could have changed this since RS.
Lack of decent prizes for BP to many expensive plushies and no tms or anything important that you need repeats of, again thank god you can clone lol.
Emerald has so many cool islands from mirage to all the event islands and the fact to most of us never got to see them really sucks,
They could have least done rare random days when a tv anouncement says mirage island has been spotted that day regardless of the ID thing, also I think that after obtaining all the gold symbols and the gold shield, Scott should give the player a master ticket or something granting you access to all the event islands, what better way to reward such an ordeal and allow you to go places normal trainers are not, the events would still have been the only way for the majority and for the few dedicated it would have been nice to have an alternative.