Defensive structure is a huge component of goaltender success, and goalie styles also align better or worse with defensive styles. There's probably a reason that Thomas only really experienced success when he was playing behind Chara for 25+ minutes a night and a fellow complement of relatively stout defensive d-men. Canucks activated their defense and drove play through them all game long. Boston played a less possession heavy style and their defense stayed at home to dedicate all their efforts to boxing out and containing high percentage scoring chances/cross-ice passes. Thomas could not sustain success with his aggressive, attacking style in any other setting, hence his late arrival to and early departure from the NHL. All things considered, Luongo is without question the better goaltender. In fact, suggesting otherwise is completely ludicrous. He succeeded under many, many different structures, on strong teams and very weak teams, with high shot volumes and low. For the Canucks alone, he was robbed of the Vezina in his first year, when he carried them to the playoffs and through a round while being shielded in a way much more similar to Thomas under a tight checking, highly structured, defensive system on an otherwise bad team in transition. He was simply a better all-around goaltender who would represent a strength on any team he played for. Thomas was not that, plain and simple - in some systems, he would have been absolutely terrible. He wasn't playable as a starter apart from roughly four years on a team playing a particular style with a particular personnel composition, under which yes, they did capture lightning in a bottle.
This isn't hard, and isn't complicated or even controversial for anyone who understands the dynamics of the position, which is littered with 2-3 year success stories that turned out to be mediocre at best under different systems or in different situations for exactly these reasons.