The question is not who will be better next to Yao but which one helps us most WHEN Yao goes down with his yearly season ending injury. I think the answer is Bosh.
We need a big guy who can best play along side of Yao and in place of Yao (for relief and for in-case-of-injury). We need the in-case-of-injury insurance AND a complementary player who can be on the floor with Yao at the same time. But I'd be happy with either of those guys if it could be made to happen. ;-)
Wow I just realized both players barely average a block a game. What's up with that? Its a really tough call, but if I had my choice, I'd vote for Bosh. Bosh is younger for one. Amare relies more on his athleticism for his game and players of that nature tend to be more injury prone. A lot of people like to bring up the Nash/Stoudemire/Shaq failure, but I'm not too sure how much fault you can place on Amare. Shaq is just, well, old and was unable to keep up with the Suns frantic pace much of the time. I also question how good Amare would be playing with a shoot first point guard in Aaron Brooks, assuming he isn't part of a deal. Additionally, Bosh is a better on the boards and IMO a better post player. It sure would be nice to have another solid post player when teams front Yao.
Zydrunas Ilgaukus has become a very durable player since his early career foot problems. With advances in modern medicine and experience with the Rockets training staff with the situation, I see hope that Yao can become a durable player the rest of his career. Maybe we'll never see the 25 PPG and 12 PPG MVP style Ming again, but I'd be more than happy with a 18 and 8 on 55% from the floor Yao. Especially if he's willing to sign a long term extension for 8-9 million incentive laden contract. I think its well worth the risk. Think positive people!