Tom's intelligence complemented Sonny's emotion, and so the two could work as a team. Michael's strength, like Tom's, is intelligence. Thus Tom, like Tessio, would eventually become a rival to Michael.

It seems likely that Vito saw Tom as a vehicle to provide Sonny with brains, so that Sonny could run the family and Michael would be free to pursue legitimate activities. When Michael joined the organization, it was only logical to switch Tom back out to the legitimate side.