I love that base for all the reasons you listed and the exposed brickwork. It’s my favorite base. Is it called the Underground?
How big is the Zephyr? I know it has two levels. In the beginning of season 4 they indicated that Coulson and Mack basically lived on the Zephyr for weeks so there have to be bedrooms, but I don’t think we’ve seen them like we did on the Bus.
I think Lincoln was kind of a boring character and his death is what made him memorable. He and Daisy flirted in season 2 but their relationship pretty much started off screen between season 2 & 3 and I don’t think they had a lot of good times together. I liked when he would use his medical skills and work with Fitzsimmons. I know he has powers so IMO it makes more sense for him to work in the lab and only do fieldwork on specialized assignments. Not everyone needs to be a field agent. To your second point, someone on Tumblr pointed out the Sousa is Daisy’s only long term love interest that hasn’t physically attacked her. Also, it’s Sousa, he’s great.
I’m at the end of season 4 and it can’t be said enough, the Framework arc is amazing. Season 4 overall is great because of the way everything ties together. I didn’t really think about this the first time I watched, but there’s no in story reason why the Framework is set in the season 1 timeline, where Ward and Trip are still alive and Daisy still goes by Skye. Unless the point is that without SHIELD everyone would be alive.
I feel like from here on out the villains get progressively worse.