Skill tree is planned for permanent upgrades, but many different abilities are tied to the seal system. How long/how many in-game days have you played? I actually have good reasons for keeping the jump abilities separate. I guess you could think of them as guns in fps (you don't want one gun that does everything).
people hate Time Limits
I am well aware of that. People hate many things.
instead of just Losing, you could instead let people keep playing and just earn less Gold
That would make the game much slower and grindier instead.
the hardcore do or die time limit
If you find yourself running out of time, it is better to go back to the entrance and cut your loses short. It's up to players how deep they want to explore, and if they feel confident enough to do objectives. Risk - Reward.
And finally, lots of mechanics and menuing around. This will probably be tidied up in time, but I recommend focusing on trimming it down and narrowing it as you go along.
It actually got much better already. It's going to be an ongoing battle.
Thanks for trying it out