-Every boss is impossibly hard
Not true, I've beat the game. The bosses are harder yes, that was the appeal for me. But they aren't impossible.

-Rydia doesn't learn Meteor until level 80
Unless you really want to grind that high you don't need Rydia to know Meteor. Many enemies just counter it anyway. My Rydia did not learn Meteor. Bahamut ftw.

-Every enemy has an incredibly annoying counterattack move
All enemies' counter attacks are caused by doing something specific, so stop doing whatever causes the counter-attack.

-Many enemies have an overpowered non-magical attack (scorch, anyone?).
Either run away or fight these enemies and get to higher levels.

-Cecil's Dark ability has been nerfed--it no longer hits all enemies
His Dark wasn't really useful in the first place, so there really isn't much change here. You'll only have Cecil for as a Dark Knight for about 3 hours anyway.

-For that matter, EVERYTHING has been nerfed
Yeah, Yang's Kick is ruined. :rolleyes2

-You can no longer play as anyone at the end of the game, and the Lunar Ruins stuff has all been omitted
You couldn't play as everyone in the original. That was a special addition to the GBA just like augments are to this one.

-Squeenix has the gall to think you'll play the game through a second time (okay, that's not really an argument).
I'll be playing through it again for EoFF Plays next month. I intend to play both the DS and then GBA version for speed completion. Sometimes there's also a "SNES on a SNES" completion so I might need to do that, too.

Also, FFIIUS did have ATB just so you know.