It would feel better for the player if you could better choose your class since what class you get might not feel like it fits them. (Like I didn't feel my class fit me at all because it is the opposite of my personality).
It would be better if it was more obvious that the cutscene was a hallucination. It really isn't apparent.
There is a very simple way to do it. Remove the wrong characters from the party. Use something like what you have to assign crew members. Have a slot for ground party members and a slot for ship party members. Enter an area where you need a different set of party members and the game can remove party members 2-4, add the first 3 party members of the other party based on the assigned party, remove the first party member, then add the 4th party member. If the slot is blank, then it skips that slot. It is so simple that you can almost do it without a plugin or script.
Just try walking around. The only things that are solid in the temple are space, water, and the pillars near the start. (and technically the ship and the player).
What I mean by gold is the gold ores. You need 50, but the game doesn't show you how many you have.
The moment of silence is long enough that it feels like the game just froze.
There is an easy way. Just look at games like open world games where you have a defined goal while still being somewhat open. They almost always have some sort of quest tracker that tells you what your important goals are. You can do this with key items that tell you what your current goals are, hidden items to mark completed goals, a plugin that shows you quests....
Another thing: Clean up the menu clutter. You have a ton of menus and you can easily condense them if you are using plugins anyways.
Have one menu for formations that just lets you deal with your ships and crew. (each module or w/e can just automatically reset or the ship could show you inactive slots and let you move crew out, but not in. This would make reorganizing much easier for the player). In that same menu, you could set up your ground party and then you just need an event or script that searches for these things to change your party.
You could then add a menu that lets you look at your questlines and see completed/in progress/all or whatever.