After clearing out bunkers through missions, the only reason currently to return to them is for the loot.
I’d like this to change. While I like the idea that bunkers are a good (the best?) source for loot, repopulating them with more encounters would make it far more interesting. Perhaps a new type of enemy exclusive to these places, that stalks/hunts you in the dark corridors. And while you’re at it, make them a lot scarier!
Take a look at the S.T.A.L.K.E.R. games for inspiration when it comes to building up suspense in the underground areas!