howdy!
I just finished my first game in 2015 (but with using backups of save games, thats probably cheating...). I have some comments to make:
1. I also had that rebasing problem (didn't try 3.06 however). In the end I regularily had to dispand my squads to be able to rebase them with 'T'. What about making a new dialouge when pressing 'T' where you can choose either between certain squads to rebase, or the squadless, or a list of everyone, the latter two options meaning that you have to choose specifically whom to rebase?
2. About the elite liberal law thing that comes up in the end game (sorry I am based in Europe), isn't it a little bit strange to have conservative judges deported to foreign countries in a ultra liberal free speach loving utopia?
3. I came to a point where I just wanted to see how my actions would influence the future events. But I didn't like to use the disband the LCS feature, cause then you cannot see what happends until the end, and it's more fun to see how the government etc. changes to elite liberal over time. So basically I gave up to the police, came out of trial not guilty, and waited the rest of the years, talking myself out of eventual attacks by the CIA or the corporations.
Maybe you should be able to watch events unfold after retiring?