Two bases with spas? Is that really needed?
Once you have troop transports with sufficient speeds, you should be able to do everything out of just one main troop base - at least that's how I'm currently playing. Troop base is in europe, which gives the least flight time if you want to go everywhere. My starting base (in north america) still has the A team, but they are doing less and less missions these days so don't need a spa there. If they get really exhausted from a mission, I can always send them to the spa base for a few days for quick regeneration. As soon as you hit the transfer button they count as beeing in the spa base.
My troop base in europe is currently at: 4 hangars, spa, onsen, medbay, library, surgery, two prisons, large barracks, small barracks, vault, beast den, hyperwave decoder, workshop.
Thats 145 living quarters and 75 workshop space. Currently only at 65 runts, the rest is filled with troops (and the few brainers to fill the lab space). In the hangars I have a jetbike, a fuego, a turtle and a convoy. Occasionally I swap the convoy out for a shadowbat (put 4 guys in convoy, send it to patrol just beside the base, transfer it to a hangar in another base. The convoy has so much fuel it can stay next to the base for days, and you can switch it back in an instant when you need it, or just for an hour to refuel.) Once I have a STC fusion drive for the turtle it's probably fast enough that I don't need to do the shadowbat/convoy switcheroo anymore. For space missions I do the switcheroo with a pachyderm.
Long term plan is to change to advanced living quarters and cryo prison (just one needed), which will free up at least one tile. Last addition will then be a cloning facility, and the vault can also be replaced by something else. More barracks, love clinic or voodo lab for example. So I will have close to max possible (only mess is missing) health regen in that base.
So far I've been quite happy with that base and haven't found anything lacking. I find it very convenient to have the active teams all in one place, to switch soldiers, armors and equipment around as I need it for each mission. The other bases have garrisons of ~10 gals that don't/rarely do missions. These off duty gals have around 12 missions done, so they have decent tu/stamina/brav/str but mostly shit accuracy. Perfect to spend long hours practising in the dojo. If I see a base assault coming, I will swap over gals from the troop base of course.