The whole base issue is kind of tricky.
If there are multiple bases, there should be a significant risk of losing them. But then you'd have to design your game around that. Base losses should be recoverable and building bases and managing staff should be simple, not tedious.
But in the end, only a small minority would suffer through a base loss, most would simply reload their game.
On the other hand, most players tend to heavily invest into a single base (design and resource wise). So if you make the lives of base-splitters easier, you end up reducing the fun for those that like to play Sims with their "megabase".
Now, if you only have one massive base, that base might never be exposed to any risk. Your game becomes making sure aliens never figure out where you are coming from. Realistic, once your base is exposed, it should be under constant attack (and basically force a game over). Which is again, not much fun.
What I would try:
- expose the main base to different kinds of threats. Think
Lobotomy Corporation. You have managed to contain an unknown alien. Before you can manage to figure out what kind abilities it has, maybe it can escape or influence your base. Works really well in a single campaign, but repetitiveness becomes an issue. Basically have base missions and events that don't stem from full blown alien attack (and without revealing the location to aliens)
- make satellite locations necessary for specific purposes. Maybe some facilities need to be built at specific locations, maybe some research needs to be done outside of the main base. Maybe the first crashed large UFO need to have a research facility built around it (one which the aliens will try to actively destroy before you finish the site). This way you can diversify the base building and still let the players try figure out clever defensive strategies, while keeping the main base as the priority for normal base building.
- put a bit more emphasis on your key scientists and engineers. If they have to occasionally leave the safety of the main base to do research at satellites, that'd give opportunities for new mission types. Could your support staff get injured? Tired? Go insane under the pressure (of you pushing the research intensity slider to max)? Maybe to simplify it, limit it to having generic staff and then appointed specialists/department heads that become requirements for unlocking certain tech trees.
- if you can't have more than one real base, that one base must have something special to it. Some layer to build upon / explore, and preferably one that can carry through several playthroughs.
But yeah, not a simple thing to balance. Definitely plenty of opportunities there. Opportunities to do interesting things and opportunities to go all X-Com Apocalypse.