I once heard a fan theory that Apollo Justice takes place in an alternate timeline that branches from the bad ending of Justice For All. You know, the one where the miracle never happen. It would certainly help to explain a few things about Phoenix; his old friends weren't mentioned because they ditched him after that case, he's so jaded because of being responsible for Adrian Andrews' false arrest and (probably) her eventual death, and that case was also probably the reason that he decided to completely overhaul the justice system; a jury could've seen that Adrian Andrews was innocent. A bit bleak, and the alternate timeline thing might bring it a bit too far into Zelda timeline territory, but it's interesting.
This still doesn't at all explain any of the story's flaws that are not related to Phoenix, though. That aspect was probably more of a case of missed potential than anything. That's pretty much what Apollo Justice is in its entirety; missed potential. Apollo had potential as a fresh new protagonist, Klavier had the potential to be a cool prosecutor with personal connections to some of the villains, a lot of the gameplay systems they added seemed like they could've been interesting... but none of them lived up to what they could've been. And that is the game's greatest disappointment; it was so close to being a worthy successor to the Phoenix Wright trilogy, but they wasted it.
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xfd dude, it's just a popularity contest on the internets.
-Vlado