I would've started off with the S-Gundam, but I thought it would've been way too overkill for a beginning suit, and I wouldn't have known where to go for the 3rd one either, since the Ex-S is insane as it is. I thought the MP-Zeta was a better choice. If you can fit it in though, then okay. 
I'm not sure he'd be likely to ally with the Sleeves due to his personal history with Zeon and Zeon-associated groups (pretty sure he'd have a strong feeling of negativity toward them for Stardust), but they could've tricked or deceived him into following them. 
That said though, It'd be more interesting to enter by something like that than just ping into existence after the timeskip without an introduction of any interesting kind. 

Anyhow, I'll have a think about it, and a re-read tomorrow - I'm off to bed now, as it's late here. 

Also, regarding the middle suit again - I did write in my BG that he was on his way to a ship with the suit aboard when he disappeared and woke up in the game universe - it could be that the whole ship came along, and was captured before the crew had a chance to come around, and S-Gundam was taken along with it, to be 'retrieved' later on.