By almost all accounts (and in my opinion) You Must Build A Boat is superior in nearly every way. Replace the word "everything" in your post with "nothing, other than Game Center integration" and you have your answer.
TBH, I've bought and played both, I don't see what's so great about them, maybe I'm not a match-3 guy but I enjoyed a tiny bit more You Must Build A Boat for all the humor and refences it has, maybe they aren't my cup of tea.
I didn't even know they were a match three game til I looked them up in App Store. I actually thought u built a boat and that sounded awesome
I largely agree with this post. I have bought and played them both extensively. YMBAB has a lot more depth and feels like it has a lot more RPG elements. YMBAB is largely time based though, which can be very frustrating if you like a casual experience. I definitely do NOT like time based games, but YMBAB has kept my interest despite that. Both games are excellent - if you like match 3 type games, I think you will like either / both.