if you hit alt f4 and choose no you'll be able to see your mouse again
I was going to plant the banner while playing as Oak when a desync box comes up, which was annoyingly coming up for a while, only this time my mouse disappeared and I couldn't click it. The box also over rode hot key commands and the options screen so I was just stuck for the rest of the game. [UPDATE] It would let me move the camera with the directional buttons and asdw. I was also able to get my mouse back by hitting alt + f4 and saying no.
Maybe they could even let us choose our skills or items if we have extra points or favor, or is that going too far? That's still a good idea though.
I actually hate how Regulus is always attacking my citadel and doing decent damage about 10sec into the game