* I've seen customers fall into the trap of thinking they don't need expensive developers because you can drag and drop, just people who can use a mouse can crack on with NiFi.
* It persisted its config to an XML file, including the positions of boxes on the UI. Trying to keep this config in source control with multiple devs working on it was impossible.
* Some people take the view that you should use 'native' NiFi processors and not custom code. This results in huge graphs of processors with 1000s of boxes with lines between you have to follow. Made both better and worse by being able to descend and ascend levels in the graph. The complexity that way quickly becomes insane.
* You're essentially programming with it. I've no doubt you could use it to write, say, an XMPP server if so inclined. Which means you can do a great many things of huge complexity. Programming tools have developed models for inheritance and composition, abstraction, static analysis, etc. which NiFi just didn't have. The amount of repeated logic I've seen it's configuration accumulate is beyond anything I've seen from any novice programmer.
I ended up feeling like it could be an OK choice in a very small number of places, but I never got to work on one of those. The NSA linking together multiple systems with a light touch is possibly one such use case. For most everyone else, I couldn't recommend it.