The late-game heavy micro appears to be partially by design and partially due to poorly functioning game mechanics. Here are a few examples, with some suggestions for improvement:
1. Rookie pilots and level requirements: If X4 wants to stick with level requirements for pilot duties (auto-mining, auto-trading, etc.), then they really need to add some kind of auto-training capability. Maybe the ability to hire training managers or possibility to build a flight school or something. I mean, come on, I'm the CEO of a galactic trading empire, do you really expect me to manually micro-manage every single pilot's activities for 10's or 100's of in-game hours? It's insane (especially considering how ludicrously slowly pilots gain levels).
2. Manager assignments to new stations: Again, I'm the CEO of a sprawling empire, is it really necessary for me to personally shuttle managers around to stations? Can't I just give them a few bucks and have them take a shuttle themselves?
3. Fleet orders: This just appears to be broken, or at least somewhat braindead. I tried many times to assign military ships to the "protect" role for my large trading ships, and it basically just doesn't work. The typical behavior is that the protectors just fly off somewhere halfway across the galaxy and either continually ask me for new orders, or engage in combat with behemoth sized Xenon battleships and self destruct. This is obviously not by design and is something that really needs serious improvement.
4. Large-sized ships with auto-trading: Basically, it's just completely broken as far as I can tell. Even with a properly leveled pilot I found that all of my L sized trading vessels would just do idiotic trades, like buy 5 energy cells on one side of the galaxy then sell 5 energy cells on the other side of the galaxy, when instead they easily could have done a full-capacity trade on something else and made 500,000Cr on a single trade. This obviously just needs to be fixed. (and until it is, you are left to the task of micro-managing your L-sized trading ships yourself)
5. Transferring pilots/staff around: Generally just an unnecessary major pain in the neck. There's got to be a better way. Similar to suggestion #2 above, maybe they could just take shuttles or something? Or heck,
Ok, well, that's about it. Please take all of this as constructive feedback. I really like X4 a lot and see a lot more potential once Egosoft fixes more of the problems and weaknesses. To be honest I wish they would just put all of the non-essential features (like multi-player ventures) on the back burner for a while and focus on improving some of these deficiencies in the core game mechanics.