I'm gonna say that I like Fragile more.
It's much more instrumentally substantial, and the songwriting in general is better. Wakeman replacing Tony Kaye was a HUGE improvement. Yes's sound was almost entirely based on their musicianship and good instrumentation was essential; Rick was leagues better than Tony, which, naturally, improved their sound dramatically. The songwriting also supports the instrumentation nearly equally, although there's always room for improvisation (and I don't mean improvement), if you know what I mean. Compare "Starship Trooper" to "Roundabout". Although "Starship" is arguably the more complicated of the two (maybe not instrumentally, but the way it's built), "Roundabout" is much, much more tight-sounding. You know? It's also stuffed with a lot of artistic ideas which The Yes Album...well, just doesn't have.
Like "Cans and Brahms" and "Mood for a Day", or even "We Have Heaven", in all of its unnecessary-yet-fitting glory. Even if it seems out of place, the overlapping of Jon Anderson's vocals is brilliantly arranged, in my opinion.
And the epics are much more consummate than those on The Yes Album, particularly "Heart of the Sunrise", which, in my opinion, is the zenith of their entire career.
Just my opinion on the topic though.
Favorite songs from Fragile?
1. Heart of the Sunrise
2. South Side of the Sky
3. Long Distance Runaround
4. Roundabout
5. Mood for a Day