I think that the main difference in the transitions of both series its that AC was more linear whilst ME became broader. AC was always an action/adventure sandbox game with great combat mechanics and they maintained that while they changed the mechanics.
ME went from being an RPG/shooter to a shooter with dialog, mainly because no one likes shooter mechanics based on RPG-like progression (DX, AP, ME1) The solutions that BW took were far more drastic than anything Ubi had to face. But it was their noncommittal choice of direction which made ME2 not quite a good third person shooter and not fully an RPG, leaving a half breed that displeases both extremes of target consumers (the shooter and RPG purists respectively)
What I fear its that this lack of clear direction will continue onto ME3 with mechanics that have the same lukewarm effect.