The bugs are not that bad if you're a bit cautious.
One gamebreaker: There's an item for your control room that you can research that, for some reason, saps your avatar's health by -20 when you save. God knows why. Don't stand by the large viewscreen in your control room. Weird.
Other gamebreaker: Only so much stuff can be moved from island 1 to island 2, including loot, and if you hack, sometimes including your avatar itself. Solution: Don't hack to give yourself extra guys above the cap. And if you captured *ALL* the loot before you moved, consider killing off a few random grunts so you have like 80 guys instead of 100 when it's time to move to the second island.
Those are the only two gamebreakers I've ever heard about.
The idea is fun, but I'd forgotten how mind-numbingly boring this game can be. It's worse than DF at its worst, sometimes. Way too much of the game is "Okay, I have my evil lair built, now I need some money / I need some research. I guess I'll vaguely micromanage my minions on the world domination screen, and vaguely micromanage the agents who are trying to break in...for an hour straight...without doing anything interesting..."
I'm currently stopped a couple notoriety points shy of when the first super-agent shows up. Getting all my research done. It's boring. Maybe I should just blaze on ahead without caution...But I'll need a pile of money later anyway, so I might as well get it now, when there's less threats, instead of having to micromanage MORE later...