Sounds like most of your issues come from the game being an Alpha. A lot of those features you named doesn't really work by themselves
While this statement is true by itself, it seems like you folks are missing the main point of OP, which is not about the game not being fun because it's unfinished, but about recent releases of the game being less fun then those from 2 years ago. Actually, I agree with the OP somewhat.
I remember playing Starsector when it contained only 1 system, with 2 factions, pirates and may be neutrals (if memory serves). Yes it was too little space, too few factions, too few ships and so on, but game mechanic itself promoted pure lighthearted, relaxed joy: you started at the bottom, you killed stuff, you grew bigger, you killed bigger stuff. Not much, I admit, but it was easy, fun and enjoyable.
Right now we have more space (cool), more factions (cool) and more ships (yay, best thing evar!), but along these definite improvements gameplay got ridden with *questionable* things. I hate it when I had to prepare to a hyperspace travel as if it was a trip to the north pole, I hate that not only I am unable to replenish 100% of my supplies by looting my enemies, but that I further could dry the whole system of supplies, and what is next? But most of all, I hate customs fleets which sole excuse for existence seemed to be to ruin my hard earned standings with a faction. Now this all might be, indeed, parts of greater plan we just not see yet as a whole, but I do agree that right now, as in today, the game became less funny, less lighthearted, and less satisfying than 2 years ago.
