Frankly, I'm not a fan of the 3 player version in any case. But, having had to play with 3 a couple of times we have added a home rule:
Absolutely NO playing of Baltar in 3 player.
Adding a 2nd you are a Cylon card nearly guarantees 2 Cylons vs. 1 human. And, the odds of Baltar being a Cylon before move 4 are high. The smartest strategy for the 2 non-Baltar players is to immediately gang up on Baltar and neutralize him. The smartest strategy for Baltar is to hope he is a Cylon from the start, reveal, and get the heck out of dodge. Either way, not much fun.
The alternative is that Baltar is allowed to run free as President early on, and if there aren't already 2 Cylons in play Baltar certainly has the opportunity to create one at move 4.
You could always get lucky and a non-Baltar player draws both I Am A Cylon cards. But, the odds aren't good. Better to play without Baltar.