What i tend to do is load up 3 or so stealth starships along with the mobile building platforms (those little orbs that let you build) and a healthy amount of engineers into a transport, send it in and run out of range of most basic units. Unload and just sit for about 80 seconds while the enemy turns around and goes back to its spot due to cloaking.
Then i speed build 2 shields either level 2 or 3, (3 if I'm not hurting for resources) then just throw up 2 or 3 lvl 3 labs.
After everything is built, i just leave 3 or so engys out, pack everything else back in (besides 1 stealth starship to cover for the engys and whatnot) and just let it sit. The basic ships seem to take no heed usually.
If something does catch their attention and they attack, often times juggling shields (turning off and repairing low shields under the cover of the other one) can hold the enemy off near indefinitely.
Interesting note btw,
2 shields requires juggling, 3 shields near eachother however seem to allow the engineers juuust enough time to repair in between volleys if the situation is right
So everyone, hows your method with the new rules?