This topic is more important than most people think. Your favorite game has real flaws, and not all of them are subjective either. Recognize them and be a thoughtful gamer, or ignore them and be MovieBo-- er, a fanboy.
I'm going to do two of my favorite games: Portal and Final Fantasy 6.
PORTAL
Who the hell designs a portal making gun and expects test subjects to use it and solve vast test chambers without attaching a freaking scope to it?
FINAL FANTASY 6
It's too bad Terra was a confused but utterly NON-suicidal NON-emo Mage-Knight in this game, because people who play Dissidia before FF6 will be all confused as to why she isn't freaking Cinderella in the story and a dainty magician in combat. Yes that was sarcasm.
Every character should have had a selection of at least 8 unique, character-specific abilities, instead of just Edgar, Sabin, Cyan, Gau, Mog, Strago, and Relm (via Sketch/Control).
Sword Tech/Bushido was a *horrible* idea. Yeah, let's make moves that require me to wait, leave me party open (unless under the effects of Quick, in which I have better options anyway), and can be used instantly only when Cyan is confused! Thanks for CLEAVING MY ENTIRE PARTY CYAN.
It's fun to try and break games but it can go too far. Vanish/Doom. Quick (which makes a joke of every boss in every version of the game). Ridiculous evasion levels for Terra/Celes with the right gear. And more.
The second half of the game needed way more story, and should have had various smaller groups converging, instead of just Celes gathering people up.
Way too many collectibles, and way too many can be missed permanently. Tools, Blitzes, Rages (oh god), Lores (OH GAWD).
Shadow is wildly overrated, both in gameplay and in character. Nobody cares, sad ninja.