Can't say I'm surprised. The battle really was MD2 vs. everything else, and it fell just short of getting a majority (108 votes out of 219). The weird thing is, critics hated this game so much, and we Pokémon fans consider it the high point of the franchise outside of the main series (and maybe even including the main series).
Conquest finished a very, VERY distant second with 35 votes, and I'd like to say I expected much more of a fight out of it, but after conceding so many votes to MD3 in the gen 5 poll, it was clear it wouldn't be in contention. Nonetheless, I think it's the second choice of most MD2 voters (myself included), and Ness Prower explained why perfectly in the comments of the gen 5 poll:
It is a fantastic game despite being THE most outlandish crossover ever.
We in America were asking ourselves, "I would not have seen this
coming! Will it be any good?" Then it came out in Japan, and that was
replaced with, "This game sounds awesome! When are WE going to get it?!"
We got it, we loved it, and you know the rest...
It's true that Pokémon Conquest has the most screwed-up family tree out of any game. It's a crossover between Pokémon and Nobunaga's Ambition (two franchises that have absolutely NOTHING in common), with clear influence from Samurai Warriors which is itself a spin-off of Dynasty Warriors. What.
The two "console series" titles present in the poll fought fiercely for third, with XD just barely edging out Stadium 2 25 to 24. And then it was a frantic rumble between the other three games to NOT finish last... a dubious honor that went to Snap with 8 votes, just behind the TCG with 9 and MD1 with 10. (Really? 10 people like MD1 over MD2? I'd LOVE to see the reasoning.)