Trey's playing has evolved a lot over the years. He does use a lot more pedals and effect than he used to. the 90s-era is very much the pure Trey tone all the way. But as time's gone on he's added more tools to his kit and that's definitely affected their jams in various different ways.
Fare Thee Well really revitalized Trey, with 2015 marking a turning point for Phish in their current era leading to them reaching the late-career peak I think they're in the midst of now.
I think the biggest virtuoso in Phish is actually drummer Jon Fishman. He's an incredible player. The dude is steady as hell on the kit. Always right in the pocket. Some of the phish drum parts are absolutely nuts, and he pulls them off like they were nothing.