Colette asked me to explain about modding the game a bit to make less of a pain in the ass here you go.
Open up Assets.zip\Assets\Scripts\StartupPlatform.lua
Do a find/replace for "DEBUGS_ON = false" to "DEBUGS_ON = true"
Save and you're finished.
Go back to the game and when you're in the planet menu(where you can see the ships flying around and stuff), press F2, that's debug mode, let's you do a bunch of useful and hack the gates without doing the minigame.
Press F7 and you go through all the different ships, want the death star right off the bat? Keep cycling till you get what you want.
This next script stops the gates from unlocking randomly.
find/replace from "self:Unhack" to "--self:Unhack"
There's other things as well that can make the game less frustrating, for example maybe you like the hacking minigame in which case you need could mod another file to give yourself 999 seconds, there's also a way to make the gems fall a lot faster but both of those would require me to post a huge script line.
This at least allows you to eliminate some of the more annoying stuff and enjoy the story and puzzles.