You flatter me, puttin' so much work in t' edit my flawless posts into n00b-glorifyin' gibberish.
Why, I'm glad you asked! Some other obvious mistakes include:
Lack of good plot shit
Lack of plot up 'til BW was intentional. You saw what Chunsoft did with Pogeymanz, there's boundless potential for plot in a game with 649+ characters (speakin' of Mystery Dungeon, you have no right t' diss this particular spin-off series).
Failure to correct obvious GTS issues (such as people requesting a lv.9 and under Mew)
... If legitimate cloning is taken out, my shiny cloning shenanigans will be a moot point. I don't want that. ;_; 'Course, I obviously understand the point of anyone anti-cloning. Yours as well.
Failure to make a multiplayer battle mode (at least, in Gen V, not sure about Gen IV) that matches levels AND allows you to use all six Pokemon
Insistence to keep making mediocre spin offs as opposed to things like Pokemon Stadium 3, a new 3D console game, etc. At least, this is an obvious mistake to me.
See above comment on Mystery Dungeon.
That, and milkin' the franchise with shitty spin-offs isn't as horrible as ya think. Game Freak hasn't developed any of them. Their manpower is completely focused on the mainstay RPGs, nor do they have anythin' to do with the disasters that are Ranger (Almia was alright though), Pokemon Channel, etc. The only real drawback to franchise-milking is the tainting of reputation.
Failure to make triple and rotation battles prominent in game
Been a problem since the introduction of Double battles. It certainly is worse with Triple/Rotation though, I don't think there's a single important plot battle that uses 'em... I concur, it's unacceptable that we're always doin' single battles. Sky battles will go the same route sadly; understandably so since not all teams have a leveled Flying-type/Levitating Pokemon, but sad none the less.