It's hard to say for sure at this stage, since the more detail-oriented mechanics are still at the pre-prototype phase. There are a variety of models I have in mind, but I'm not sure which one will be best yet. I really prefer systems that don't need to be automated, but at the same time I really hate late-game turn bog down. Particularly with combat and just managing too many units for it to be interesting. The differ we between the early game and late game in terms of fun of combat is pretty stark in most 4x titles for me.
Anyway, so that's the chief problem with most 4x games that is on my hit list: keeping the late game streamlined and moving along quickly, in terms of mechanical things the player has to do. The amount of info should of course be more complex than at the start of a game, and the decisions should be tougher, but how much extra clicking you have to do shouldn't be going up logarithmically.
Automation is how most 4x titles solve this, as you note, but I'm not a fan of that, as you again note. I'd prefer to have underlying game mechanics that simply take the early and the late game into consideration better. I have a variety of ideas for how to do that, but I don't know which one will be best, or if I'll have to come up with something entirely different from any of them due to what we find of during the prototyping phase.
Incidentally, and this is from a different genre, but I feel like SimCity nails the early game and late game transition. It gets increasingly complicated, but it doesn't get more automated (in SimCity 4 and before). Instead, it just isn't designed in such a way that you have to keep re-making the same decisions over and over. So mainly you are making new decisions, with the occasional revised former decision. I really prefer that to trying to automate a repetitive set of decisions.
Anyway, there are a lot of things that are still in experimental or even on-paper stages for this game, which is why it's not ready until next April, heh. But I am happy to be just sitting in this one genre, rather than splitting genres, because it lets me focus on what I do and don't like about this genre, and try to design something that hits as optimal a spot as possible in there. I think that's why AI War worked out so well, is I took that attitude toward RTS. We'll see what happens here!