I got tired of managing my way around the channel system of AE2 after a while. I switched to Logistic's Pipes for quite a while and while it's a bit more expensive than AE2 in some respects, in others it seems to be a bit more powerful, given it's integration with Buildcraft. I was never quite able to get the hang of Project Red Transportation.
As for Refined Storage, it seems to have the same problem AE1 did, with a one cable to rule them all mentality. Which isn't a bad thing on it's own, but eventually you reach that point where: I've done all this before. I'm in this new pack, with new things, but I've done all this stuff before. I can automate this or that, and I don't have to work at it, because I've already done it before and worked out all the problems there. Ultimately, I end up treating both as a storage mod, a super sized chest, and then do the 'work' with other, more fun mods.