Medrex

I always assumed the reason behind designing motherbase all spread out like that was so that if they got attacked again like with the first motherbase, the other platforms couldn't be as easily compromised.

With the platforms that far apart an attacking force would have to have to either spread themselves out thinly to attack multiple platforms (giving the defenders a much better chance of resisting them) or they'd have to take a much longer amount of time attacking each platform (giving the diamond dogs more time to set up defenses/regroup/evacuate). The only way to overcome those problems would be with an overwhelmingly large attack force which would have no hope of hiding their approach or disguising themselves as some other entity like last time.

Setting up explosives to take out all of them would be made much more difficult too since with that much distance between them, it's pretty much guaranteed that none of the platforms rely on the others much or at all for stability, so you wouldn't be able to take the whole thing down by taking out a few of them like Fatman could have with the big shell.

Finally it's a hell of a lot harder for random people to travel between the platforms unnoticed so if some mole was trying to set up some sabotage ahead of time, their movements would be more obvious and more likely to be questioned. For example, it'd be kinda suspicious if a guy from the medical platform dropped by intelligence, security and RnD in a short period of time for nothing really important. If the platforms were closer together that wouldn't be as weird.