Intel's such an ideal location because he can easily create conditions that can cause them to be forced out of action, be it being killed, snapping in action or screwing up so severely they're removed from the field - though keep in mind the kind of thing that'd get someone expelled from the PPC entirely is probably a really serious crime, not something he could create unless he frames them for something.

What's that about "no Mary Sues allowed in HQ"? They're not allowed to run around freely, no, but the reformed Sues have just as much self-determinance as any other character, provided that they're taking all of the necessary measures to prevent relapse, such as the use of Logicillin and help from the Psychs, and the Sues that are being tested by the Psychs and the DMSEAR are kept restrained or in stasis when there aren't any tests taking place. There are plenty of ex-Mary Sues that are agents here. That's not really all that much of a problem. While I can see some people being suspicious of an ex-Sue agent because of her background, it wouldn't put someone who made an agent out of a Sue on some kind of watch list.
To another point, since PPC policy means that Mary Sues aren't considered truly sapient, while it might be unnerving for an outsider to see someone experimenting on them and putting them through numerous mental modifications, the higher-ups wouldn't get one of the scientists in trouble just for doing so, especially if the PPC gets a new agent out of his research. The department is called Department of Mary Sue Experiments and Research, after all. The experimentation is a big part of their job.

For the last part, though, that makes more sense. The DMSEAR doesn't have a lot of active scientists, so not only would potential danger to any of the lab workers would need to be cut down as much as possible, it would make sense that they wouldn't send someone into retirement after he'd started becoming unstable, they'd just keep him away from the current tests and subjects and such so he wouldn't mess anything up. His scientific knowledge could be important in the future, after all. Yet, he'd gotten so attached to his work over the years that he keeps coming in when no one else is around, just trying to finish his last project, and he either does not know why or can't remember why everyone is always trying to get rid of him. There's character potential in that.

Thanks. Glad you found the suggestion useful. Us newbies have to stick together against the killjoys in the old guard, right? (And you'll find I'm very good at thinking up story ideas, but hate the process of turning them into actual stories. So I'll probably come up with some more suggestons for you.)

Hmmm... A rogue Flower. That gives me an idea...

Really? I must not have come across that one. I'll check the wiki page.