Personally, the "problem" I and a few others I know have with CFD is a combination of things.
To play shadowrun, you need a certain suspension of disbelief, just like with battletech.
The matrix, creatures out of tolkien books, etc.
Then came the nanites, and every techsavy person should be screaming "it doesn't work that way!". But you can make do, for it's a small part and fluff and ingame effect aren't specifically connected.
But apparently, someone at Catalyst saw it the same way, and his brilliant Idea was "let's gate this unbelievable thing behind something even less likely! That'll show 'em!". Yeah, I can't see how that could possibly backfire.
So now we have Nanites housing a sentient AI, individually capable to matrix combat, able to reproduce, reprogram other nanites of any kind, and directly manipulate a human being on a cellular level far better than science has managed to in a few millenia, all without any previous experience with the matter.
It's a bit jarring, like in every book there's a disclaimer "Hey, don't you think roleplaying is a really dumb idea? Why don't you go out and enjoy the weather? I mean, this is so silly!". It really continues the problem that started with the missions for "new players", in just slightly overdoing it.
As for the actual mechanics we now finally have, it can be used for opponents, or plot hooks, so it has a place in the world, so I can't complain about that, still, when I see a CFD section in a book I ignore it. It's best not to think about it too much.
Edit: One more thing about the actual PDF:
In older pdfs (till RF), the books had an extra "Cover page", so that's my base setting. But DT and CF don't, so I need to change my settings every time I'm watching those. Maybe that could be fixed with an actual TOC taking up two pages.
