As stated several times above, Hughes is a legend in his own time, but there's really no contest IMO. I have maaaaaad respect for what Hughes accomplished, but end of day, I think one could surmise that while Matt Hughes was a wonderful wrestler who BECAME a wonderful MMA fighter through his gift, GSP is a wonderful MMA fighter whose only becoming a greater all around fighter.
A big issue for me with regards to Hughes and his "greatness" also goes back to level of competition. I mean, if you look at alot of those 40-however many wins over his career, there isn't alot of sizzle to those foes. In short, his record's pretty damn padded. Then you get into his WW title run and while it's impressive that he held the belt for so long, I take issue with the quality of some of his challengers at the time, as well as alot of the UFC's weightclass organization at the time and the amount of solid potential challengers that were at PRIDE instead. Also, people can harp on GSP "not finishing", but Hughes too has gone to some decisions over his career against some fellas who weren't world beaters.
I think that GSP right now is fighting the best that the WW division has on the planet(sans a few expections) and is completely dominating, whereas Hughes dominated, but I don't think they were the greatest the world had to offer, which again all goes back to the era.
MY MMA RANKINGS
HW Velasquez Cigano Werdum Cormier Bigfoot Barnett Mir Browne
LHW Jones Machida Evans Hendo Davis Goose Teixeira Shogun Mousasi Bader
MW ASilva Rockhold Belfort Weidman Jacare Okami Kennedy Consta Belcher Boetsch
WW GSP Hendricks Condit MacDonald Diaz Maia Fitch Kampmann Ellenberger Pyle
LW Bendo Alvarez Maynard Melendez Thomson J.Miller Diaz Pettis Chandler Grant dos Anjos
FW Aldo Mendes Curran Lamas Frankie Zombie
BW Cruz Barao Fernandes Faber Moraes