Porto to Lisbon bus or train?

First, regarding Flixbus - I’ve taken it at least three times in recent years from Cascais to Porto and have never seen the bad things you mention. My most recent trip was last July. The bus has always been clean and had great working AC. I’ve had one piece of luggage ( rolling carryon size) that I did not pay extra for. The small carryon ( very large purse size) was with me on the bus. There are smallish shelves above the seats but don’t think a larger rolling carryon size would work.

The trains are a bit more expensive but it you purchase ahead of time, the price goes down. There are areas at the end of the coaches for a limited amount of luggage. And there is room for fairly decent size carryons in the back of the seats. Difficult to describe. There are overhead shelves also, if you can lift the case over your head - I can’t. I have seen luggage in the aisle on occasion but the staff might complain if it takes up too much of the aisle. I have put my luggage at the space at the end of the coaches many times with no difficulty.

Either mode of transport is quite good and very inexpensive compared to any other European country in which I have traveled.

We took the train (I think the company was CP), and there were overhead luggage racks which easily fit carryon size luggage, as well as racks for larger bags at the end of each car. Your larger than average carryon bags might fit in the overheads, but not sure how people in neighboring seats would feel about you potentially using so much of the overhead space? But it may be fine too. On the train we were on, the racks at the end of the train actually had cable locks to prevent luggage theft (for a couple euros).

We had the same experience Barbara G had when we took the train from Porto to Lisbon in November. Our suitcases were a little too large for the overhead area and we put them at the end of the car where there was a luggage rack. We just kept an eye on them when the train stopped at stations.

My wife and I did the bus in reverse direction than you are asking. Lisbon to Porto (airport). Middle of the night and I did not think to see which company it was. Overhead storage for carry on luggage. Worked out ok except for the marathon walk from the bus drop off to the terminal counters.