Here's my thoughts. I love the extra dungeon because now there's a reason to attain higher levels than what's needed to beat the last boss. It's something extra.

You want to turn off the extra dungeon? Don't visit it. Problem solved.

Now, the magic system, changing it into one pool instead of individual magic points per spell level, I don't like. I find it as big, or bigger, a change than changing the equipment system from the original version.

Regarding the magic change, they should allow you to revert to old school style. That is of course hard to do and keep the numbers, so it should be a choice at the very start of the game to avoid the glitches that might be involved entirely. Also, they should add the option at the very start to choose the retro equipment system (invididual party members holding stuff, limited space for it too). That'll keep everyone happy.

Again, extra quests I like (you can just avoid those anyway if you want to stick with the original, but hey I know you won't be able to avoid the temptation of beating up Kefka or Sephiroth with your level 50 warrior ), but the gameplay, if they want to change it, should always have an option to revert to the classic style.

If they are really changing the gameplay a lot, and do include options to go classic or original mode, then might I suggest giving thief/ninja the ability to steal stuff (again, it can be shut off and all).