I have been playing Dwarf Fortress a bit and think that this style game would be a great project for a BYOND single player game. I haven't tried this style of game and was looking for suggestions on some design issues:
Player management
World Generation

Player management- I like the larger, open ended style more like Dwarf Fortress than Dungeon Keeper. Conceptually, I envision players save individual worlds. Each world has one expedition team. If the team gets wiped out or retires, the players may start a new one and embark to recover the old location or start anew somewhere else. Teams I don't really see any way that this would work multi-player, unless, maybe players who join cannot be in the same region. (Big world divided into many regions, each region is a playable area generated when entered and then saved).

World Generation- Again, I like the broad options, smaller focus idea. So, the world would generate a big map, say 100x100. Each tile would be a region (playable area) whose terrain is largely determined by the big map. So, a region marked mountain bordered to the north by other mountains, west by a water region, and south by forest would actually have all three features. Regions would probably be a fixed size (x,y) and variable depth (usually positive Z limited by elevation, negative z capped at a max depth, say 15 levels?) Additionally, each region generates rivers, lakes, and other local features. How, I am not sure... I am also not sure how to generate a believable big world map.

Interface- This one is vexing me greatly. Since the player will be managing an team and not be personally represented, I assume the best way to handle this is via some sort of not interactable, invisible mob. Clicking on stuff activates it and brings up their context menu. A minimap that you can click on to cover ground quickly ala many RTSs would be very neat- no idea how to do that and not really a priority.

Any thoughts or suggestions from anyone who has experimented making an RTS?
I've tried my hand at it, and would like to get into one again someday. I think the key thing for any RTS is good troop management. Ways to easily select groups, pick out individuals and create fairly elaborate actions without much mouse clicking or button knowledge. It helps take away some of the tediousness of campaign management.

If this would be strictly single-player, I'd suggest using as many of the mouse interface procs as you can. Drag selection boxes, drag and drop upgrades or munitions. Click to attack or break off and retreat, right-click to access actions, things like that. Make it really easy and intuitive, and the rest should fall into place nicely.

I've found most RTS games are fun in and of themselves, though many suffer from bad troop management. Dune 2, my personal fav in this genre, had really lousy troop handling. You had to click to select a unit, click a command for that unit, and then often you had to click a target for the command, like where to move or who to attack. Sending a large group of tanks to the enemy as well as coordinating repairs and resources became a bit tricky and very clicky once you started to get into numbers larger than a handful of units. It was one of the first RTS games, and really helped to define the future of the genre, so I cut it some slack.

Were you thiking of having a stationary base to work from, or more of a nomadic tribe of explorers? I think the latter sounds really neat, and would fit better with a single-player game than multiplayer.