I wish it would show you, with a glowing light or something like that, which code it was currently running. That way, you could detect the problem code easier, and also fix it easier.
I think you should have an unlimited amount of slots and upgrading should be free. This would encourage players instead of grinding for hours just to upgrade something, they would actually go and buy boxes to upgrade with.
I wish you could assign priorities to buildings, because it's annoying to build a bunch of buildings, like 11 reactors, and wait 5 min for 1 of them to start working, whereas if you could assign that one top priority, it would get finished first, instead of all the orbs be distributed to everything.
Everytime on each of these Decision games (Both Decision 3 and Medieval), my progress isn't saved, I haven't cleared my cache, and I save everytime after leaving. It's ridiculously annoying because I had nearly completed both of them too.
 "Mechanical Commando 2"){kind=icon}
 "Toss the Turtle"){kind=icon}
 "light-Bot"){kind=icon}
 "Mud and Blood 2"){kind=icon}
 "Pwong 2"){kind=icon}
 "Monty's Moon"){kind=icon}
 "Supermechs"){kind=icon}
 "Exit/Corners"){kind=icon}
 "Viricide"){kind=icon}
 "Vector Runner"){kind=icon}
 "Reaper of the Undead"){kind=icon}
 "Ether War"){kind=icon}
 "Outpost:Haven"){kind=icon}
 "Home Story: 1971"){kind=icon}
 "Shopping Cart Hero 2"){kind=icon}
 "Endless Migration"){kind=icon}
 "Road of the Dead 2"){kind=icon}
 "Creeper World 3: Abraxis"){kind=icon}
 "Decision 3"){kind=icon}