To comment on a few of your points,

1. IMO that really does not effect the scale of the game, it's not limiting the amount of places you can go at all, just hop somewhere else on the planet and you're gonna find similar things. You arent really meant to use the ship for such a small distance aswell, and the instanced wall to wall distance is really quite far for being on foot.
2. Eh, it was your choice to fast travel. They included a ton of fast travel options cause not everyone either has the time for the game otherwise or they just does not care about the flying around in space part as much. But the option to not fast travel, and to instead use your ship is there 100% of the time so I don't understand complaining about it, it's just a matter of choice.
3. I personally found the menus really easy to use and get used to, but I was on controller and not kbm, cant speak to how kbm feels.
4. What you are describing as a lazy intro is the exact intro that bethesda fans want in these games, quick and over with so you are quickly released into the world to figure things out on your own, it's what bethesda does every time.

But yeah agreed on the technical aspects, except for new atlantis looking horrible. If anything looks borderline horrible for me, it's the borderline uncanny valley faces everyone has.