Blocking the player from taking a follower, especially with a randomly generated environment, means either the follower is left behind or the player has to wind their way back out of the level (potentially through multiple floors) in order to address the challenge by re-equipping. I don't know if that's horrible, as it may force players to haul lots of crap to deal with variable contingencies. That could be good (balance say looting vs. equipping) or bad (micromanagement).

I think not breaking stealth is quite important, maybe they try to stay in cover if you're sneaking, and the enemies ignore them unless they do anything too blatant.

Something like stealth might have to be solved with level design. Maybe there are set challenges and clearing rooms where followers can gather. You could take a few, deal with some sentry or trap or whatever, then summon the rest of the followers onto the next room. It would probably lead to needing lots of abandoned areas, like empty barracks or storage areas, which could be okay I guess.

As noted above, I think it will really be bad if players occupy the same space. I remember an Aliens console game that did this and how weird it looked to see a half dozen colonial marines all merge and demerge from the same spot. That was using 3d with an isometric camera, so I think FPS would look even worse.

I agree that would suck... you could use soft avoidance instead of hard collisions. For example the NPCs could avoid each other in pathfinding using influence maps. But it would still leave open the option of passing through each other temporarily. Another possibility is only allowing greater pathfinding flexibility when an NPC is behind the player or more than a certain distance away.

As noted above, I think it will really be bad if players occupy the same space. I remember an Aliens console game that did this and how weird it looked to see a half dozen colonial marines all merge and demerge from the same spot. That was using 3d with an isometric camera, so I think FPS would look even worse.

Check Prison Architect. They can occupy the same space but they "don't like it". They also do all pathfiniding on a traditional grid but move around as a free move. Best of both worlds and looks very decent.

Perhaps it would help if we had more information about your goals for this game? For example, why does the player have so many followers, and what is the player expected to do with them? How does the player interact with followers, and what do they offer to the gameplay? Is this like a party RPG, with each follower having individual skills to contribute? A military game in which followers may be expendable grunts? A survival game in which followers are to be protected? Something else entirely?

Otherwise, another possibility that I don't think that I've seen suggested yet is the "Terrifying Teleporting Watson", as seen in the Frogwares Sherlock Holmes games, I believe: followers remain stationary (or mill about, or perform tasks) while in the player's view or not required to move, but simply teleport to a point just behind the player when too far away and not being looked at. It looks really odd at times, but it should in general avoid the problems of pathing and leaving followers behind.