This is a summary of a game I ran briefly a long time ago. I think it was pretty enjoyable and you might be able to steal some ideas.
Beta Complex is a riff on Paranoia using the Shadowrun rules. Specifically Shadowrun 4a, without any of the magic. Paranoia can be played straight, but its rules are really lacking in a lot of areas. There is a reason I’ve never met someone who played RAW. Shadowrun 4a is my go to RPG for games when I want mechanical complexity, that aren’t fantasy hack and slash. If you remove all the elves, and spirits, and most of the setting there isn’t actually a lot more mechanically you have to do.
Broadly, the plot was straight forward for any group who has played paranoia, and can be summed up with the intro sentences I sent to the players. “We learned from the disastrous Alpha Complex experiment, and reprogrammed a brand new Computer. Welcome to Beta Complex.” Essentially, we ran it that Alpha Complex, the game they all know as a slapstick failure was the first test. This is the second, and its being played straight. The PCs are still R troubleshooters, but their task is less mundane, and less lethal. Instead, they are sent to infiltrate secret societies and shut them down or rat them out.
The PCs are 6-7 generations into Beta Complex and starting to realize the system is rigged. It looks to them like the UV has taken control, and set the system up to be awesome for him and no one else. Stop him, fix it, or escape?
We did introduce mutations and instead of having them be random and generally worthless, used the metagenetic qualities from Runners Companion to cover mutations. It was still forbidden, but it was at player discretion.