I'm unconvinced zombified computers are the way to go. Why not just build a legitimate supercomputer of your own? It's easier, less likely to attract attention, more secure, and probably more resistant to catastrophe.
My view has always been a fairly high-tech, but competence-light Foundation. In conventional technologies, I agree with Scantron. Their real strength is in technologies which they're the only folks that know about, like memetics and certain other mildly supernatural things. Generally more advanced than commonly available, with a few instances of supertech.
Of course, they need this technologies to not just completely fail at their job. The way I see it, the Foundation can't be that big. Even with amnesiacs, the Foundation can't have more than a few tens of thousands of people, including D-class, working for it at a time. Otherwise, it will become public knowledge. Foundation scientists aren't the best of the best. They are the best of the folks that the Foundation finds out about, attempts to recruit, and who are willing to work for the Foundation.
Since they have to be prepared for anything, the Foundation has an enormous amount of breadth. But since they aren't all that big, they have basically no depth. Consider NIH, one of the best health research agencies. They have about 15,000 employees. They just do conventional health stuff. The Foundation has to do health, cognitohazards, military, engineering, construction, facilities management, and so on. They can't exactly contract stuff out easily. It's impossible to do any of these things at a standard competitive with a public, dedicated agency such as the NIH or the special forces branch of basically any halfway decent army. About the only thing the Foundation is the best at is weird mind stuff, and that's only because the very existence of those isn't public knowledge.
The fact that the Foundation is so spread out has some other problems. Say an SCP is found that's a leopard that drives anyone who sees it insane. The cognitohazards folks claim it, of course, because insanifying is obviously their division. Then they get utterly stumped. If the biology folks had gotten to look at it, though, they'd immediately see that the insanifying is actually due to a toxin that the creature's pheremones are laced with. And that's not even getting into divisional or site-based rivalries that make things even worse.
The Foundation needs its advanced technology to brute-force its way through these obstacles. The insanity-leopard broke free? No problem, we have robotic soldiers that can get close enough to contain without succumbing to the pheremones. Similarly, the Foundation probably needs a lot of support of major governments, especially in this day and age. It's not really practical to obtain all the weaponry they have without attracting attention, and next-generation stealth won't allow you to recover SCP-682 from Kansas City without the US government taking note.
I actually kind of view the Foundation as inherently doomed, and in denial about this. The internet in its current form means that if every single security breach isn't crushed immediately, it will become public knowledge. If you told 100 random people around the planet something the Foundation didn't want getting out, it could not stop that information, even if you told it who those people were. The only thing it could do would be to spin the information as something else. The increasing number of contained SCPs force the Foundation to grow ever larger, ever closer to the point where it can't possibly remain secret any longer.
The question is how far the Foundation will go to stop itself from becoming public knowledge. I don't see any way for that to be done short of resetting civilization back hundreds of years, which is a temporary solution, a dangerous solution, and one that's probably not possible without killing billions. And I'm unconvinced that even the 05 are ruthless enough to do that preemptively without a clear and present danger. Plus, setting back civilization that much would basically destroy the SCP Foundation in a few years, when all their technology becomes completely unsupportable, and every scientist has to be trained completely from scratch.
It'd actually probably be for the best if the Foundation went public. I don't think the panic would be as bad as some alternatives, and it would remove some of the barriers to effectively containing these things. Of course, it would be best if it were done in a controlled, gradual manner, rather than an all-at-once, catastrophic, security breach. The only question is if the Foundation would be willing to go along with that.
Wow, this came out a lot longer than I had expected. Er, did what I say sound reasonable?