As far as ships to command for a Commodore with a low Contribution Rank, the YZ-775 (Dangerous Covenants) is Rarity 3 and not a total loss as a combat vessel.
But I think Keith's also got a point in that for most starting groups, you're not established/trusted members of the Rebel Alliance. You're still fresh recruits (Contribution Rank 0) and you don't really start being "trusted" until you hit Contribution Rank 2, as discussed in the GM chapter. At CR2, a Commodore PC will probably be able to request (or be assigned) command of a smaller cruiser, like a refitted Consular-class light assault cruiser, or maybe a CR90 corvette (both Rarity 5), since they've at that point proven themselves to be a capable and most importantly reliable member of the Alliance. Capital ships are pretty hard to come by for the Alliance, and so they're not going to just hand out Nebulon-B frigates or MC80 cruisers to just anybody.
That being said, maybe we'll see a couple of Rarity 4 cruisers in the eventual Commander sourcebook so that a group with a Commodore doesn't have to wait two full Contribution Rank increases in order to get command of something other than a Lambda shuttle or light transport.