You can probably pick which boat you want to put your admiral on. There's probably more units in his boat 'cuz it's a bigger boat than the other two.
The idea now is that Generals will not be an unbeatable charging melee unit like they were in previous games. Especially with cavalry being much less effective in Empire.
Back to this, generally Admirals put their flag on the biggest badass ship in their fleet so we can expect Admirals to be in the thick of the fighting unlike their land based counterparts.
In some cases Admirals did either prefer a faster, smaller ship or wound up transferring to one when their big ship was damaged in battle.

Also the number that shows is the number of guns not the crew strength. You can see this in some of the videos where you can see tooltips showing both number of guns & number of crew.