Honestly, I think the most disappointing thing about the game is the cross-save feature. Everything else is great. The mechanics and the story still hold up, the graphics have never looked so good, the voice acting is what it is (they never claimed they were going to improve it), and finally getting the International version here in the US is a dream come true.
The cross-save feature? Is a overly-difficult, unintuitive pile of crap. I can get over having to manually start an upload. Automatic uploads would be awesome, but I can deal. But having to go back to the main menu to do it, with no way to get back to the main menu without resetting or closing the game? Bull crap. They already had to hijack the Save Game command to send it to the Vita's save mechanism, why couldn't they have added an "Upload Data" option or button or something there? Not to mention that every time I go to upload, it's somehow changed which saves I told it to sync and uploads out of date saves, so I have to manually choose which save(s) to upload every single time. Then the obnoxious fact that it doesn't preserve the timestamp on the save files. I keep five saves in case I need to backtrack, but when I send them back and forth between the Vita and the PS3, they end up with the same timestamp (the time I synced the new files to the new system), so I can't tell at a glance which is the most recent. The whole cross-save function in general just reeks of lack of playtesting.
It just pisses me off that I make progress at work during lunch on my Vita, but then have to spend 10 minutes of my limited play time once I get home just to be able to start playing on my PS3, and then make sure I leave enough time at the end to go through the reverse process just so I can play on my Vita during lunch the next day.