Really interesting thread on what to choose for your first cap ship. I haven't personally (ever) used a colony cap ship, though now I'm really thinking about it...
http://forums.sinsofasolarempire.com/309106I'm really impressed by the point that (in the initial explore / expand part of the game) you can actually colonize a planet WHILE you're clearing the gravity well of neutrals. Otherwise you'd be waiting until after (or nearly after) the fight (since neutrals seem to target colony frigates if you jump one in) to jump in the frigate. Then you wait for its anti-matter to replenish enough to colonize, whereas the larger stores of antimatter on a colony ship apparently allow it to colonize immediately after jumping.