I guess its a matter of having a smaller readership... More people read shounen than seinen - just look at the number of posts (or threads, or even sections) in the Shounen section of MH compared to the Seinen section. Sad as it may be, shounen somehow seems to draw more fans and gets more attention in general.
I personally have yet to read Berserk (I am going to... Soon), so I can't comment on it. I love both One Piece and FMA a great deal, but I went with FMA simply because it's such a complete package. Not because it's a completed manga, but because of all its different aspects and facets that made it such a good manga. Action, comedy, heartwarming-ness, philosophical life questions, romance... FMA really had it all, imo. It made me sad to see that the gap between OP and FMA was so big. Well, at least FMA won the Staff vote :3
yeah, we have a lot of manga better than the big 3, but competition between the big 3, one piece win by large margin ....
The problem is that the Big 3 are mainstream; many people who read one of those manga tend not to know of others. Big 3 can be seen as the manga to introduce others to the world of manga, and you usually have new readers that have either read the Big 3 or prefers it over other manga, not to mention wanting to be loyal. If I had not gotten into Naruto and Yu Yu, I'd have most likely voted for Dragon Ball since it was naruto that got me interred in manga.
However, that Berserk and Death Note (yep I know that Death Note is a Shonen, don't worry) ended up so low surprises me a little, especially for Death Note which is pretty much a classic.