I think it might be fair to say Smile (had it been put out in something kinda resembling its 2011 form) would have been more complex than anything the Beatles put out. I mean, most songs on Smile were these "pocket symphony" type things put together in different segments. The only Beatles song around the same era which did that was Day In The Life (I don't consider the Abbey Road medley to be the same thing).
On the other hand, while the meta-structure of most of the songs on Smile were fairly complex, the (what I'll call) "micro-structure" of all the songs was actually quite simple, consisting mostly of just 3-chord tunes (check out the Wiki article on it). On the other hand, Beatles songs tended to be filled with more chords than your usual pop song, as this essay
here explains.
Granted, I have no doubt Brian Wilson was more than capable of writing songs with complex chord patterns (he had already done some of that) and I've no doubt either Lennon or McCartney could have written their own "pocket symphonies" had they desired to (McCartney in particular did some of that in the 70's - think Band On The Run). So when we're comparing the artistry of the two bands, they're kinda similar, but different. And in the aggregate probably about the same.
As for weak spots, that's pretty subjective. Personally I think Run For Your Life is a great (if mean) song, though I suppose I can see why others think it might be filler.