If IIRC, Jaqen was in that prison cart as someone fleeing from King's Landing, shortly after the first sword of Bravos met his unfortunate end to Meryn Fucking Trent, right?
Yoren supposedly had the prisoners while Syrio was still teaching Arya. For Syrio to be Jaqen Syrio would have to beat Trant, then sneak into the dungeons, kill a prisoner that Yoren already had, dispose of the body and take his place. That seems unlikely. There is also the issue of Faceless Men not killing for sport or convenience. Syrio/Jaqen would not kill a prisoner just to stay close to Arya. And at that point Arya was not hooked up with Yoren either, so Jaqen/Syrio would not know she was heading north to the wall and would have no reason to jump into a prisoners face to stay with her.
There's also a fairly big problem with Syrio being a famous, well known person in Braavos and later being an established and respected water-dancing teacher in Kings Landing. He was there for a while before Arya came to town and their relationship struck up. It's pretty crazy to have a Faceless Man there in an assumed identity for years without anything special to do.