I would like to know REALLY what makes it so much inferior? Is it mainly the single ship thing? Or what?
It was basically that they didn't know what made their previous games interesting, and removed those aspects accidentally. Instead of an expansive universe, you get a very small area of play, with very constricted routes through this area. Instead of being able to manage fleets and essentially become your own faction, you have to babysit your other ships. Within just a few hours of play, your personal ship is upgraded to the point of being able to take down capital ships; after which the game simply runs out of upgrades for you.
A single ship is just fine, even with less upgrades than this one had. In X3, I used the starting Mamba fighter the entire time I played. The difference between the two is that the Mamba felt good. It could perform well in combat due to excellent maneuverability, and had a first person view which was unimpeded. And the AI would use them too, so it wasn't like I was some special snowflake with deus ex machina powers magically imbued into my ship. Meanwhile, the ship in Rebirth is a plot asspull to explain why your ship is superman. But then it's about as fun to fly as a brick. It's given a crappy name
which is even described as a prank in-universe and which every NPC points out and laughs at. (up until this recent update) It had about 50% of the screen obscured by "cockpit" which may as well have been dead pixels. And the UI was so awful you couldn't even tell which direction a hostile was in, or if there even were any. Not that it matters, because again, your ship is superman; which means combat is so dull and menial as to be meaningless and actually boring. And then there was the NPC 'co-pilot' who was less endearing than opening your clothes drawer and finding each and every one of your socks stuffed with a mixture of slugs and severed baby fingers. So yeah, I would be perfectly fine with a single ship if it were merely a mundane, run-of-the-mill Mamba or something.
Overall, it wasn't really any one thing, it was just a case of horrendous design decisions piled on top of one another.