Going forward, Fallout may wind up taking the lead, as it has many newer fans, and Metal Gear is kinda finished now.
As of right now however, I would have to go with Metal Gear. It's been a staple gaming franchise for a longer time than Fallout. MGS1 was considered very revolutionary, and did things that few games had done before. Fallout 1 may have done something similar, but not to the extent Metal Gear Solid did. Metal Gear has its legacy to ensure some high level of popularity. Whatever Fallout's legacy is, it can't be bigger than Metal Gear. At least, not yet.
From a personal perspective, when Fallout 3 became a big deal, the only thing I remember saying was, "I never knew there was a Fallout 1 or 2!" By no means am I talking trash on Fallout as a series, but I had never heard of it till 3 came out. Even long before I touched a Metal Gear game, I knew about the series since it was a franchise you would hear so many people talk about constantly.
I don't really have a horse in this race to begin with. Of the two, I've only played Metal Gear Solid games, but it's not a series I really love. I've never had any interest in replaying them, which is a personal indicator of whether or not I like a game. I certainly respect Metal Gear, and I imagine Fallout is pretty great considering its relatively newfound popularity.