Hi, I was on that inaugural flight, and most of us were traveling from Minneapolis as a group on a religious activities visa (to network with and help Cuban churches in our denomination), except for a couple of people who were going to visit relatives.
The restrictions have been relaxed a bit, but you still can't go there legally just to lie in the sun at Varadero.
Yes, check-in did take a long time, because they were training in new staff, and they had cake and coffee for us at the gate.
Since there were so few passengers, most of us had a row to ourselves. Only cold, non-alcoholic beverages were available, but they served a ham and cheese sandwich.
On the way back, we went through no extra scrutiny landing at ORD. I just told Immigration that I had been in Cuba on a religious activities visa. I had the paperwork to prove it, but the official I talked to didn't ask to see it. When I went through Customs, the official just asked me what I had bought, and I told the truth: a couple of CDs (legal under a religious license) and some craft items made by members of the religious denominations that we interacted with. He just waved me through.
They are mainly on the lookout for attempts to smuggle in cigars, rum, and coffee.