Well, the game is awesome and I loved it, but there are a number of things I disliked or that could have been done differently IMO.

Aeons
Bahamut or Valefor should have been water aeons, probably Valefor is the best choice since he is found at Besaid. My thoughts would be a large birdlike creature (as Valefor is) formed of mist and constantly dripping water. Two non-elementals is too many.

Magus sisters, this aeon I hated. Now, Anima is a dark aeon right? Well, I personally think the Magus sisters should have been 'light' or holy aeons. When I heard of the Magus sisters I thought to myself that they would be like three mysterious robed sisters, would have worked better than some dumb (and one very fat) bugs. The idea of them all having different attacks and having to be requested to do something is a good one though, but I still didn't use them, I just maxed out Anima.

Sidequests
The secret Aeons and the various sidequests were pretty annoying and VERY obscure, one of the few I found myself was Yojimbo because I was curious as to what was down below that bridge where Defender X was, this lead to me finding the rusty sword but not knowing the hell to do with it.

The only other sidequest I managed myself was the Cactaur village when I went back to Bikanel to get the creatures, I ran into the sign and the clue led me to the oasis.

But the others? Who would think of dodging 200 lightning strikes in the thunder plains to get a Sigil? I didn't even know you could get anything from dodging strikes let alone bigger better prizes!
Anima was a nasty one too for several reasons, firstly the Baaj templte being an unknown location, it should have been mentioned at one of the temples and as a result appeared on the air ship list IMO, isn't the destruction spheres challenge enough? Speaking of which I did not like Dark Valefor, unlike most (maybe all) other Aeons Dark Valefor can't be avoided, much to my dismay as I tried to get the icon I missed in Besaid. It was only thanks to a post here mentioning the use of Yojimbo's Yanmato that I managed it.

I think all other sidequests were just horribly obscure since most would not have been obvious to me in the slightest, I doubt I would even have stumbled across any of them myself and instead would have completed the whole game entirely unawares had I not read about them when finding out how to defeat Sinspawn Gui (yes I got stuck on it )