Would Protoype and CI be slow?

[eluser]Jelmer[/eluser]
It will increase the footprint of your website, though that has nothing to do with CI or using it with CI. Everything extra you load will increase your footprint.

But to go into your question "Would Prototype and CI be slow?". Probably nothing slower than Prototype with any other kind of server-side support code. So it comes down to Prototype itself, I've been using it extensively for 4 months now and I must say I'm quite satisfied with it. So to answer your question indirectly: CodeIgniter & Prototype are both excellent frameworks which I would very much recommend based on by experience with both and using them together.