dtgreene: Every now and then, a game gets remade, and while many remakes are faithful to the original versions, there are many that are not, to the point where they are arguably different games entirely. For example:

SaGa 3 (the game I'm playing right now) got a remake on the Nintendo DS that drastically changed the game mechanics. Among other things, levels and experience points were removed, being replaced with a system where you get a chance of stat growth after every action. (There were other drastic changes, but that is probably the most blatant one, especially since it interacts with many of the game's other systems, like the transformation system.) (By contrast, the SaGa 2 remake preserved the original's mechanics with some minor tweaks.)

Ys III: Wanderers of Ys got a remake (Oath in Felghanna) that changed the game from a 2d sidescroller to a 3d platformer. There were other major changes, like completely changing the role of rings. (In the original, rings were like those in Ys 1, except that you had limited ring energy and there was a ring that made you invincible.)

Lufia 2: Rise of the Sinistrals got a remake that changed the game's genre; the original is a turn-based RPG (and is actually strictly turn-based, with no action elements), while the remake is an action game like the Ys games, from what I've heard. (I haven't played the remake.)

Any others that you can think of?

(By the way, I heard that Fire Emblem Gaiden got a remake; can anybody tell me whether that remake has weapon durability, and whether spells cost HP to use?)

darthspudius: Brutal, poor tinyE. I much preferred it to Uncharted. Those games have so much potential and fulfil none of it.

durandl: Syndicate.

EA thought it would be cool to turn this game into an Ego Shooter, luckily they failed horribly. Sad for the franchise though.

CARRiON-XCII: ...why did you have to remind me of this bloom-infested nightmare?

codefenix: The 3D remake of Final Fantasy III differs pretty drastically when compared to the original. It has altered/nerfed (but still unbalanced) job classes, revamped job growth, and fleshed out the four main playable characters (who still have no real personalities or backstories pertinent to the plot).

I personally would have preferred a 2D remake closer to the FF Origins release of FF1 & FF2 on the Playstation.
Supposedly such a remake was planned, but ceased development early on. Too bad, because what they released instead (in my opinion, at least) looked instantly dated compared to other 3D RPGs at the time.

dtgreene: One thing the 3D remake did right was to make the Bard class useful. Another thing it did right was to make the Red Mage job useful end game.

One thing the 3D remake did wrong was to make status ailment spells useless.

One thing the 3D remake (specifically the DS version) did otherwise was to make it possible, via flaws in the map's collision data, to temporarily skip parts of the game, and to become permanently stuck. (In one playthrough, I got the Sage job early and was able to use summons without sacrificing other magic.)