I love the
potential AJ has, but I think it falls behind its predecessors for two major reasons (and there are more than 2, really, but these are the things that strike me most).
1) It feels more like buildup to the next game than a complete story: there are several loose ends that aren't addressed or are pushed aside and the whole thing felt like one big set up for a sequel to me. As such, I thought the conclusion was lacking.
2)
Nothing ever happens to Apollo or anyone he cares about*. On the one hand, I was pretty happy to see the attorney's assistant
not getting into constant trouble for once, but when compared to the crap Phoenix had to endure through a significant amount of his trials, Apollo gets off really easily: you don't see him running around frantically to save his best friends' lives, or having his own life threatened by one of the "truly guilty parties", or falling off of ___. Even the main villain, who is quite possibly the most demented character to ever grace the Ace Attorney universe, never directly goes after him. And I feel like those lowered stakes diminished the entertainment value of the game.
*
- Spoiler: open/close
Not counting Nick-gets-hit-by-a-car here, as not only does he not seem to like Nick very much... it's Nick. The guy couldn't get killed off if he was hit by a speeding train and flung into the Grand Canyon.
As for my favorite case, at least pending the arrival of my copy of AA:I, I always flip-flop between the last case in T&T and the last case in JfA. The former was brilliant, but I spoiled myself rotten before playing it so a lot of the twists lost their impact for me. In contrast, I didn't know ANYTHING about JfA before playing it and I was on the edge of my seat the entire time.