Yeah, with the sort of scale you have here, "microing" can still consist of shifting groups of 200 guys around at once.
There's just not many cases when it's ideal to be moving one ship at a go. Usually engineers will do their own thing (except when you want to assign them to a dock or whatever constructor permanently, for instance).
Speaking of which I'm still recovering from the grief of finding out that I shall never have a fleet of 150+ Tech III Engineers again.
In an unrelated note, I think I encountered a couple of odd AI bugs.
I took out the command center of one place and a the usual stream of Tech III ships flew from the wormholes/resource points towards me... and then stopped. I scratched my head, waited patiently for a couple of minutes as more of my ships flew through the wormholes to re-enforce; I dragged in a colony ship and built a command center; built a Tech II engineer to do some repairing; pulled in a few science labs to do a bit of research; and the AI sat there. Interestingly my Ion Cannon I had taken over also didn't fire during this time, but I'm not sure if that's because there were no Tech I ships left, or reinforcing wasn't happening, or it was busted as well.
Eventually I lassoed my ships and sent them flying towards the enemy AI, and when my ships got into range they woke up and started attacking and such. Quite odd.
Second bug is that I went in on another world, took out the command center, and ran back to my home wormhole. Except I miss-clicked and my ships overshot it and were way on the other side, with only the cruisers in attack range of the wormhole. Given it was 90% Tech I and Tech II cruisers since most of the other ships are a little more fragile this wasn't actually an insignificant force, however I expected them to be swarmed by the stream of ships that were almost up to them when I noticed them, before they turned around and ran back through the wormhole. So I swapped back to the other planet and frantically bolstered my defense leaving them to sit there and distract for a bit before dying painfully.
Except they didn't. The AI ships flew up... then delicately parked themselves on the wormhole, in range of my ships, and sat there patiently waiting for their allies to show up so they could all assault at once as my cruisers (Tech I and a few Tech II) took them out (Tech II, III and IV) faster then they arrived. I think I lost half a dozen ships, but wiped out 100+ without any issues.
A new tactic has been discovered! Though it is probably not intended...