Terranigma: The magic system is ALMOST completely useless, tied together with a collectathon for the means to cast more spells (but why?).
FFVI: Horrific balancing that makes a drunken elephant on a tightrope look graceful.
Tales of Phantasia: The only legitimate version(s) we Americans got was the atrocious GBA port with its near-soulless translations and its delay between your inputs and the actions in battle. Meanwhile, we never got the superior versions. But hey, at least we get a laugh from the end of the world being called the Kangaroo due to a translation error (probably the best thing about that translation, ironically).
Tales of Symphonia: So very many of its tropes became cliches the moment this game first came out, making you question if it's worth it to give a damn if anything's cliche or not.
Wild Arms (original game): It's so easy to cheat via item duplication that it isn't even funny, and you can max your stats early because of it, eliminating what little challenge even existed in the first place.
Wild Arms 2: The English translation, full stop. Also Tim.
Wild Arms 3: The pacing tends to put a lot of people to sleep, or turn them away, before they can enjoy the best fights or the fantastic story. Also, 97% of the main story seems to end at the 3/4 mark, so the final arc drags a bit with a seemingly out-of-nowhere villain reveal despite her being there all along.
.hack//G.U.: It takes so damn long for Haseo to grow into a tolerable character, personality-wise. So, so long.
.hack//I.M.O.Q.: It really has not aged well, both graphically and in terms of controls.
Super Metroid: I have to compare so many other games in the series to ITS standard, even the first Prime.
Metroid Prime (and Prime 2): I have to compare so many other Metroid games to it/them, including Super Metroid. Also, jumping platforms in first person is a bit of a butt.
Star Ocean 2: It takes an hour or so of unskippable scenario and dialogue for the game to truly to begin. Yet, that's not the worst thing about the game. The worst, and I can almost not forgive the game for this, is
Bowman.LoZ a Link to the Past: It's not "Link's Awakening" or "Makora's Mask"
LoZ Link's Awakening: It's neither "aLttP" nor "MM."
LoZ Majora's Mask: It isn't "A Link to the Past" or "Link's Awakening."
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