it says right in the release notes, there were changes to the standard shader. So if you authored textures before, they are going to look different now. at this point it looks very close to Marmoset Toolbag 2. Which IMO is a good thing. I have not tried the Metal/Rough workflow yet, so I cant speak for how that one looks. But spec/gloss still works fine I think they just changed it. it may be an issue with substances? did you try baking them? substances have been a constant source of pain during the unity 5 beta, i would just bake them out for now..