Oh, no, he's definitely got major flaws (of the condoning the use of a soul-devouring Ghost Type violence against an enemy and disrupting peaceful negotiations because he's too cynical to believe they'd work, being a backstabbing little manipulator, and generally having a really poor grasp of morality because he essentially says justice doesn't make sense to him aaaand while that incident's been dealt with, the source of it all is still there: he made a conscious decision years ago to repress emotions/shun forming bonds because he believes they get in the way of personal growth and his all important goal of becoming Strong).

Even at the very end of his storyline, he still enjoys being cruel a little too much (he blushes watching his now-friendly rival's Pokemon being beaten and suffocated) + when asked if he's living up to his own Pokemon partner's love for him, he says he's beginning to.

So his development there is incomplete. He has a cruel streak, questionable morality, and is only beginning to break out of his own self-imposed isolation that led to all these major flaws. I think a game like this would be very suitable for getting him to really connect with others and respect life more. -- things I should save for an app, why did I think it was necessary to say all that here... just woke up, sorry! ^^;;;

Bonus question (I know, I took a lot of your time, so sorry!) I'd imagine that'd be the case, considering the significance and nature of Glie's birds/crows in canon, but just to be certain, Pokemon cannot accompany their trainers here, correct?