He has had strong ties with Microsoft in the past with Gears of War and even gave a lot of input in the development of the Xbox 360. Epic has worked closely with MS
on multiple occasions and I am sure that Sweeney knows the corporate culture of MS pretty well. But lately he has been a bit on edge with Microsoft which means that he might know something that we don't or doesn't like the direction that MS is going in with UWP.
I don't think he has an issue with UWP itself, he's actually highlighted some of the benefits. His issue is that Microsoft could one day change their mind about it being an open platform and release a Windows 10 update that locks it all down, disabling the ability for signing by any CA root or distribution through stores other than Windows Store.
https://twitter.com/TimSweeneyEpic/status/715637147898880000