I highly suspect that this (or ideas like it) have already been suggested, but *shrug* doesn't hurt to re-hash some things.
Boarding combat - currently, 99% of all boarding combat seems to consist of a squad of highly trained, heavily armored marines against the hapless spacers aboard whatever ship gets boarded.
Thoughts (to be taken individually or mixed and matched):
1. Armory Module - perhaps with size scaling with number of crew. Upgrades typical crew from light weapons and half racial armor to regular weapons and racial armor.
2. Robotic Defender Module - provides X number of defensive troops for the ship. Default with same stats as a normal infantry, with a possible upgrade tree that can lead to heavily armored or heavy weapon variants. Could be RP'd as either actual robotic troops, or as automated boobytraps / hidden turrets in the ship.
3. Ship Security Module - a module that can be filled with X tons of troops, selectable from your currently researched ground combat templates. Set in the ship build menu. Then, when you queue up a new ship to be built, the cost of the troops will be added to the cost of the ship, and when the ship is completed, it will have the troops on board. (Basically, a troop transport bay, but without having to micromanage loading up individual defensive compliments of troops for each ship.)