I think you should put more consideration into the level of pixelation in your visuals. The character creation currently makes the character always look bad due to the size on screen, which is only made worse by the background looking so crisp. Also, the dialogue text looks like it's half as crisp as the text for who's talking, except when highlighted.
When first looking at the quest menu during the tutorial, I was momentarily confused, because it wasn't clear that I was looking at a menu. I think it was because I hadn't received any mention of how to leave a menu, so I wasn't in the right mindset. I suggest putting in a small bit of text mentioning that escape goes back, partially for that reason but also because some game quit in response to pressing escape. It's good to make it clear that your game doesn't.
When the warp rings were misaligned, I had trouble finding them, because I didn't realize there was a doorway downward from the fuel room. I think an indication on top of the walls of what sort of wall they are would help with that.
When I reached the first planet, I had the diagnostics menu up due to just exploring what was there. I'm not sure if that's why, but the menu disappeared without actually leaving the menu, resulting in the game not being responsive.
I wish GMS2 would pause while not focused. I think I made the initial warp attempt harder because of trying to type up feedback while time was still passing.