There are some perks that might cause some overlap/problems in the merge. Nothing terribly important, but I think brainstorming some solutions could be helpful. Here are some I can think of.
1. Deep Sleep/ Roughin' It
Deep Sleep adds Well Rested whenever you sleep, Roughin' It adds Well Rested whenever you sleep outdoors. Roughin' It would be useless if you have Deep Sleep and there is no reason to take it over Deep Sleep. However, they both suffer the problem of being inferior to Swift Learner, which gives 10% XP regardless of whether you have slept or not. Maybe a solution could be to have Deep Sleep work for only interior beds, but that would make both perks even more pathetically weak, or perhaps Roughin' It could do something else? Or perhaps it would be better to remove Well Rested altogether, since the New Vegas hardcore already gives incentive for sleeping and the whole "owned bed" thing can just be for convenience, or maybe Well Rested can be restricted only to hotel beds and Red Lucy/Sarah. Ideas?
2. Size Matters
Big guns is removed, so what kind of effect can Size Matters have instead of a big guns boost? Perhaps some kind of boost to big guns like 2-handed handle weapons and 2-handed launcher weapons, like reduced spread, or something like that?
I'll write down more as I come up with them.