This might be a bit of a big request and I'm not sure if it would be doable with the time left until release.
I think there should be more to separate Lieutenants from ordinary bosses.
This is rather anecdotal and usually a few updates come out between the chances I get to fight Lieutenants so this might be out of date, but from what I've seen there are already some boss types that usually only show up as Lieutenants or Overlords or are at least not as likely to show up elsewhere. However, there still seems to be quite a bit of overlap between Lieutenants and ordinary bosses.
When I encountered a Lieutenant and it turned out to be one of those "big flying machine things that shoots electricity and rockets" it felt the way it should. However, it felt very underwhelming when the Lieutenant was a Giant Skelebot or Green Amoeba because by then I would have seen so many of those.
I recently saw the "big flying machine thing that shoots electricity and rockets" (I forget what they're called) in "Boss Gang" missions and that doesn't exactly feel right to me. I think those should be saved for Lieutenant bosses if possible.
I think there might be a need to keep Lieutenant/Overlord and ordinary boss types more separate so those boss types aren't already "spent" by the time the players reach them, which might require making more boss types and I'm not sure there's much room for that between now and release.
Now for something that might be more doable.
I keep feeling like it's difficult to get NPCs with certain professions and the necessary buildings to use them early enough. A lot of times, by the time I get the stuff needed to place windmills and bouys, I'm already at continent Tier 4 or 5 and taking on Lieutenants, which limits their usefulness.
Part of this seems to be that missions that give you spell materials and missions that give you NPCs or buildings are usually separate. For some reason (and I have some guesses as to why, see below*) I almost never get secret missions to get spell materials, so spell materials take priority for the main missions that affect continent tier.
Secret missions do help with this somewhat, but they're rather sparse and much of the time they feel really random. It's really tricky to actually find what something you need this way because they seem so random compared to most other things in the game.
Maybe they aren't quite completely random, but right now they appear to be that way and that feels like it goes against how trying to acquire things in this game usually works. There is a lot of random in the game, but with most other things in the game you usually have an idea where it is most likely to occur and so you go there to maximize your chances of finding it. I haven't seen much of anything like that for secret missions so actually trying to go after them feels a bit odd. If there is a pattern then they are sparse enough that I haven't picked up on it yet (I suspect that I'm more likely to find "rescue NPC" missions in caves, but I don't know if that's actually the case or if I'm being superstitious
I think it would help if I had a better idea of where to look for secret missions that will get me what I want, like how some of the other stuff in the game works. Maybe certain regions or areas should have a higher chance of offering certain things.
Again, it may be that it already works that way and I haven't picked up on the pattern yet, but either way I'm haven't seen any tendencies that I can use to better my results with these missions.
*I have a suspect that there are certain structures, NPCs, or materials that are more likely to appear in secret missions if I don't have them yet. I tend to skip secret missions that are not offering anything I want/need at the time and that might be messing things up.