As far as I know, you're right Skeeter - the Klingons have a 50% bonus or something when it comes to troop Transports. You can take over a system more easily with a Klingon Troop Transport than say...a Federation one.
If you play as the Federation, it's generally better to wipe out the system and recolonise it, rather than capture it. That avoids all the morale problems.
Always remember to keep your Cloakable ships Cloaked, and if you're gonna have minor battles, keep them on their own. You get a completely free turn then, instead of a turn where your Cloaked ships are simply not attackable, whilst the rest are canon fodder.
