This is great stuff, thanks. I do think a lot of the problems here are framing problems and that a good tutorial to set expectations would go a long way on addressing your feedback, but also it's kind of supposed to be a little weird. Some other random points:
- "Because I have to contend with the rules of how it wants to work rather than how I want it to work."
- Considering all the different ships will have slightly different controls and handling quirks, it sort of is the intent that you learn how to work around the given control set and flying style. You might not like how one ship flies, but maybe you like another more, etc.
- "The thing I had the hardest time with in general was slowing down. There are no brakes, and while I didn't specifically expect there to be brakes while playing, it does beg the question: how does a craft that flies like an airplane and lands like a helicopter transition between the two without brakes?"
- This is a really good question, that has two answers. The first is that in the final version you have direct access to the reverse thrusters when in normal flight. This makes slowing down to hovering speed very easy. The throttle actually works a bit differently in the final version than it does here to make this a lot easier and make a lot more sense.
- The second answer is that it kind of is complicated because ironically what you're describing as a problem is actually a real problem and skill with landing helicopters in real life. When helicopters are flying at speed, they actually fly like planes, and pitching up causes them to gain altitude and fly up. This will happen in the game too if you're also flying at speed, so slowing down to an appropriate speed before going into hover mode is actually important. Knowing when and how you can start easing the nose up for "reverse thrust" is also part of the skill. This is extremely helicopter-like and I thought it was really cool, THAT SAID it is weird and inconvenient that you can't reverse thrust in normal flight, especially because this is critical for space-flight. Hence the point above.
- "I wanted to do something like fly in and bank sharply left or right and then use vertical thrust to counteract my forward inertia, but switching to hover mode cancels out my ability to roll."
- There isn't a direct way to do this, but in the full version since drag depends on the ship's velocity flying belly down will slow you down dramatically and you can do handbrake turn landings. Ship turn rates are unaffected by airspeed, so they can turn fast enough that at low speeds you will basically stop in midair from the drag.
- This isn't the most elegant handbrake landing (it was my first try) but you get the idea.

- "When I was in the tunnel I was trying to switch to manual mode"
- The tunnel is actually exactly what the training missions are going to frame as something specifically for the hover mode, since it's about very precise maneuvering in a very tight space. It doesn't make sense to use the manual mode for this. In the full game, one of the types of hangars the player needs to be able to fly and land in are very tight vertical spaces and manual mode is just not meant for that kind of maneuvering. Honestly I think "manual mode" is a bad name for it, because it implies that it's meant to be a "full control" superset of what the hover mode does and that's just not the case. The "Hover Mode" itself has changed names like 5 times so far, because I'm not exactly happy about that either. I almost wish I could call it GERWALK but nobody would get that.
- "I'm not so confident that it makes sense to have aerodynamic lift"
- The aerodynamics is exactly where all the interesting difficulties come from in the flight model, so it's non-negotiable. Mastering the transition between forward flight and hovering flight is one of the most important and difficult aspects of flying a helicopter, and that's the kind of feeling I wanted to get across. Also even a brick will be affected by aerodynamic forces, and depending on the ship, some ships will be more "bricklike" than others. The prototype transport is the generic everything ship, so it has enough aero to be interesting, but is mainly focused mainly on the hover mode stuff.
I know it might sound like I'm arguing with these points, but this is actually really encouraging because most of the parts of the game you're describing as being difficult are supposed to be difficult and take some practice to really get right. The game is about nailing sick landings, and if it was super trivial to do, what's even the point of the game?
As I said before, I think a lot of the problems are coming from incorrect framing and expectations, and I think with a decently designed tutorial (and tutorial level) a lot of that could be ironed out. That said there are some control oddities that I'm not exactly sure how to handle. Space raises some very annoying questions and is essentially two more control modes even if it wasn't intended to be. That will require more testing.
It's also important to note that in some cases the omissions of certain features is very deliberate because it would go against the very thing I'm aiming for. E.g. I actually did try having direct control of forward/reverse thrusters while in hover mode (there's video of it too) and it looks and feels atrocious, nullifying everything I thought was interesting about the control and flight model.
Thanks again for trying this and noting it all down! You always come at my games from a very different place, and always give very detailed and insightful feedback on how a normal person might (or might not) survive contact with them.