When you enter a system, the enemy tends to attack the first ship you send in. Tell your capital ship to jump first, so that it takes the brunt of the fire. This way your escort ships won't get killed off.

Your ships tend to attack the enemy flak frigates first. This is horrible, as flak frigates are both very durable, and they are harmless to your ships. Focus your fire on the LRFs, heavy cruisers, and light frigates. Leave the flak for last.

There's no reason that kind of fleet wouldn't be able to take on local militia. But keep in mind that the best planets (terran and desert) have the largest militias to fight. It's much easier to grab an asteroid/ice/volcano world early on, and they will give handy XP for your cap ship to take on the tougher planets.