Well, abilities can now have up to four levels (instead of just three)...most (maybe all?) ultimate abilities will have 2 levels as well, so a lvl 10 cap can only max out it's ultimate and 2 of its 3 abilities...
The level six abilities can be purchased twice.
Because those other abilities can get researched up to level four, and the level six twice, you can see a level ten capital ship with only three abilities to use. To be honest, this will make for much more interesting game play. When faced with something like the Advent's Propagator, how will you know if its primary function (for that player) is to colonize and revive capital ships, or to be a battle ship?