I use a mix tactics when taking over systems.
The AI is well known too send all there forces into your system when the command station is destroyed, so the main threat when taking over the system is that one massive force.
Like the others suggested, I use Raid Starships, they are fast and a major asset too my military.
I take out anything that respawn enemies, that means all guard posts and what not. I send only the Raid Starships, rarely I send other ships for a mire distraction.
Then I take out the Warp Point and Command Station, then that lovely AI Armada will pour into your system you are attacking from.
Luckily I tend too have my Command Station as far away from the Worm Hole I'm attacking, using Spider Turrets and the all mighty Triangle ships (Fighters, Bombers, Frigates), The Armada usually never gets half way too my Command Station. The only time ships do get past they are usually high in health or cloakers, which die with in seconds of meeting the Wall of turrets humbly waiting for them.
Its a long elaborate plot I always use but it gets the job done, steps awhile too set up and then after that's done you still have too worry about the turrets.
I have discovered a cunning plan too avoid the turrets tho. All you do is destroy the next system before you colonize the current one, this way the Turrets will have no incoming supplies from the AI and will be disabled. Now it becomes shooting fish in a barrel with your Triangle fleet.
I find it has the least amount of casualties and faster than the pea shooters.
Hope that my strategy helps ya SilverHammer and gives you new ideas too taking out those challenges.