Is it better to make a 2 tier wedding cake with 1 3 inch layer or 2 2 inch layers?  I plan on using a mousse filling, so I would have to cut the 3 inch layer in half.  But by using 2 2inch layers, that will make it taller.  Need suggestions.

What's wrong with taller?  You don't want short and squatty.  Ordinarily, they should be at least 4" tall.

Two 2 inch layers is the standard for tiers.