To be fair, the tweet doesn't say he was happy with the changes per se - more that he wasn't unhappy with them. (IE Neil's done adaptations for film/TV so I'm sure he is both pragmatic about it and understands the business.)Allegedly Neil was happy with the changes for American Gods, and was not why Fuller/Green were fired.
https://twitter.com/neilhimself/status/959783773511520256
Bryan Fuller needs someone business-minded who can reign him in, because he's definitely able to produce some great things.
As far as I know, Hannibal was a fairly low budget show (which is why NBC kept it for so long.), but Fuller seems to want to do much more with a huge budget.