I'm not particularly bothered about the reactors as they stand -- yes, you can turn them on instantly, but during the heat of battle do you notice the need to? Often the destruction of an unexpected reactor can give the AI the brief window it needs to do something really nasty, like kill you. This, in turn, creates a lot of strategic decisions about where to build your reactors, how many to leave on, etc. They aren't huge, but they are a part of the game. And, the current setup of reactors (in general, not relating to automation or not) is something that encourages players to take more planets, which is important. And neither Mark Is nor Mark IIIs are useless by any stretch, especially with certain playstyles that use lower numbers of planets.
At any rate, they aren't something that I'm inclined to do a major overhaul on. For those who are newer to the game, you might not know, but these were already majorly overhauled back in August or so, with a lot of community feedback and ideas on there. For now, I'm feeling pretty happy with them.