The 3DS games (especially Spirit of Justice) give Apollo some really great moments. Admittedly Phoenix's attempts to steal the spotlight never entirely go away, but Apollo ends up really stealing the show for a lot of people in the end. By the way, make sure you play the fantranslation of AAI2, it's absolutely phenomenal, and my second favorite AA game!
Finished AJ, I liked it! I don't compare it to The Trilogy because that had 3 games to build up it's combined story. The only thing I would change about AJ is getting rid of Wright and developing Apollo more. I'm enjoying Investigations now, but I can't wait to see where Apollo goes in future games.
You bet I like AA! I hope you enjoy AJ, it used to be quite divisive among fans, but opinions have cooled over time, and a lot of people love it now. Apollo is a really fun main character in my opinion!