Here's a small one, and probably a non issue for the most part. I restarted a fresh save after 3.1.2 (mostly because of the maintenance cost buildup problem that others have had) and everything is working great so far. I have only had two issues:
1). For some reason Sanctuary had a maintenance deficit when it was in the positive for cap generation (+6 vs -3 at the time). It only did this once, and I assume it was because of the new generator system that was built (whatever is giving 192 power), because now I have a black smoking conduit on the top of the Sole Survivor's old home which I can't repair. I paid off the deficit, and it hasn't happened since, but it is still there.
2). The HUD widget doesn't seem to like updating certain things. Or, more to the point, when I go away from Sanctuary and come back it shows the status of Sanctuary back a few days ago. IE, slightly short on water (which was rectified) and full defense (which went down as a result of fixing the water) and the %upgrade thing shows 15% when I last left it was actually at 54%. When I go into the settlement build mode and back out, it updates the HUD to the appropriate values (including any increase in the %upgrade since my last visit), but I just thought this was a little weird.
Minor note, the revamp of the skeleton has two Brotherhood of Steel type power armor cages down by the "police station" now, but one of them is located in a less than ideal position for getting back into a power armor. Maybe have them nudge it out a foot or two.
Like I said, both of these are probably small, non issues. Just things I've observed.
EDIT
As for anybody having issues with duplicate leaders, do be careful with it. When you cycle through leaders, it will show duplicates of certain ones that are installed on different mods. For example, the Sturges one shows up in both COOTS and Uituit's Junk Town update, which are the only leader updates I have installed so far. When I picked Sturges to be the leader for Sanctuary, I was a doofus and picked him both times, thinking it wasn't a duplication bug because I don't know why I thought that. Well, it went through the flyby mode with the music playing, then about 3 seconds later a SECOND iteration of the song started. For the most part, aside from the out of sync and annoying music overlay, everything went fine. Only one Sanctuary skeleton was built (nothing was torn down and rebuilt again, at least I don't think so), but once I got out, I was stuck in the song loop. Even fast traveling away didn't stop it. While I like the Fallout 4 theme music, it got old quick. I had to exit out of the game and back in to get it to go away.
Long story short, yes you can pick someone twice, so be careful, or you might be hearing the damn theme song the whole time you're playing.