Personally (and again, for the price you paid) if you like the watch, then I'd definitely keep it. It really is an unrepeatable bargain at £2700. A quick look on Chrono24 and you'll see you'd almost be hard pressed to pick up a 10 year old standard Navi for that kind of money.
As others have said, there are definitely a larger proportion of people with issues with the in-house movements compared to the old ETA based ones. Lots of threads on it, but in some ways it is kind of expected to a certain extent as there's only so much that laboratory testing will tell a company about how a movement will perform in the real world. The ETA movements have between 40 and 60 years of real world usage, so any issues have been long ironed out. Not making excuses for Breitling here at all, but new movement issues can happen to the best of them. You just need to take a look at Omega with the well documented 33** series movement issues.
I have no doubt Breitling will iron the issues out, but I think you may struggle to get them to do it under warranty. Worth a try though.
