-Every boss is impossibly hard

I don't think so. It just requires a different strategy than before.

-Rydia doesn't learn Meteor until level 80

Meteor is kinda terrible anyway.

-Every enemy has an incredibly annoying counterattack move

The enemies were programmed to counterattack certain actions in every version of the game. It's just now the game outright tells you it's a counter.

-Cecil's Dark ability has been nerfed--it no longer hits all enemies

Yes, now it hits one enemy for extreme damage, even more so when hitting a weakness.

-You can no longer play as anyone at the end of the game, and the Lunar Ruins stuff has all been omitted

GBA version only.

-Squeenix has the gall to think you'll play the game through a second time (okay, that's not really an argument).

Like Momiji said, it's just for people who enjoy the game enough to play it again. And, to be fair, the optional bosses almost require you to play through two or three times to get the augments necessary to defeat them.