I think it had more to do with choices and loyalty. Tom was family (more or less) with the utmost loyalty. Genco was pretty close to family (I seem to recall something stating that Genco's father and Vito's father were very close friends back in Sicily and that's why Vito went to stay with them).

Also, Tessio's crew was made to appear to be it's own family, not related to the Corleones, so it might have been very hard to replace Tessio as caporegime; also the point of separating Tessio and Clemenza was to prevent them from conspiring against Vito - if Tessio was the consiglieri he would have constant and direct contact with Clemenza and they could have plotted together, so I feel it was in Vito's best interest to NOT have Tessio as the consiglieri. Even if he was slighted I'm sure Vito explained it to him (Tessio understood why Vito didn't want him to associate with Clemenza most of the time) and in return Vito gave Tessio more control over his men than Clemenza had.

Clemenza wasn't as intelligent as Tessio was. Michael was supposed to be the legitimate businessman. Sonny was too hot-tempered to be consiglieri. Fredo was too stupid (not "smaht") and didn't have the force of character.

Basically, Vito didn't seem to have a choice. It was Tom or nothing.