A hotkey to select all damaged ships sounds good. Although at the moment you can use the ship selection filters to do a similar thing. Holding N and 8 whilst selecting units selects those with 33% or less health and holding N and 9 selects those with 66% or less.
I find Mobile Repar Stations and space tugs to be pretty good at what they do and generally worth the knowledge cost. They also repair faster than engineers, and can repair multiple ships at the same time. I used to use engineers to do my ship repair work, but now I find it a lot quicker (and economical) to use MRS + Tugs as the tugs quickly grab damaged ships and bring them over to the MRS, which gets rid of micro.
The issue I have with micro is more about turrets, as I find myself having to build and destroy engineers to patch up my turrets between assaults. However, the new remains system in the pre-releases tends to eliminate a fair part of that these days. Turrets turn into remains (like mines), which are nigh impossible to blow up by conventional means, and these remains are then rebuilt by remains rebuilders (which replace mine layers). You get 50 remains rebuilders (maybe more if we get another tech level of them
) so it's fairly easy to leave these around turret clusters. Turrets that are rebuilt start rebuilding at 50% in the latest pre-release, so it's fairly quick to replace destroyed clusters. The only micro really around these days is patching up turrets which are damaged, which doesn't really take too long I suppose.
I guess it all comes down to what the role of the engineer really is. Remains rebuilders and cleanup drones have taken on a lot of the work regarding turrets, and Mobile Repair Stations + Tugs are better (usually) at repair work than engineers (if that's your playstyle). I feel like managing engineer modes might encourage more micro, and it does kind of make the investment into Mobile Repair Stations a bit obsolete.
However, maybe a new Control Node could do the trick that only allows engineers to repair, not assist construction.