I actually tended to have 2-3 "main" bases once I got through the early funding problems.
I had my original which was a main base simply from having been around since the beginning, usually another "main" base in the other hemisphere with a secondary team. And finally a third, out of the way base that was where I set up most of my manufacturing and storage. Only a small token defense team, and ideally nothing should ever fly out of it to lower chance of detection.
I'd always keep a decent stock of essentials at each main base, but most of my loot would go to the storage base, usually somewhere in Antarctica. Once I got Psi labs I'd also put those at the storage base and transfer troops there in shifts to get them sorted through.
The two bases with actual teams, one would tend to end up with most of my veterans, while the other would keep a couple of veterans and just take on the easier missions, mostly for training. The vets would end up being sent on the tougher stuff. battleships, terror missions, and base attacks.
Looking back on it, there were some problems with this strategy, but it seemed to work decently, and kept everything decentralized enough that losing any one of those bases was not a big deal at all. The manufacturing base could be a huge loss, but I always kept an eye out and if it looked like things were going down hill anywhere, I'd just liquidate things quickly, and transfer the important stuff. So, worst case, I have to rebuild some workshops and my income slows for a few months.
I'm going to be somewhat disappointed if they do dumb it down like it seems they are. But I'm still keeping an open mind. I'm already hesitant about them not using squares, but I guess I'm just being a stick in the mud there.