I have two huge problems with A2, as much as I love it to pieces.
The games AI is so broken I have to severely handicap myself to maintain a challenge.
Annnd the main story/characters never appealed to me (not to mention most of them have awful character design, especially luso and cid)
Hell, if I remember correctly certain side-quest chains are longer (and FARRRRR more awesome) than the actual main-story-line itself.
I adored the side-quest. Heck, this is one of the few games I got really close to doing everything, but the story-line to me is just an obstacle to get to the next batch of side-quests.