First of all, I'm not sure if this is in the right place, I just made an account yesterday, and I'm not particularly active on any forums.
I have a few suggestions for balancing out leveling. Seeing how you can begin FNV with all skills at 100 and so on. It's rather convenient though, that the player would get shot in the head as weird as that sounds.
First of all, Intense training perks should reset when you begin New Vegas. This way, the player has to rebuild their character but in a way that would make sense after traveling through DC. As an alternative you could simply make brain related attributes decrease. Charisma and Intelligence mainly. However, Strength could also be reduced; being a courier isn't necessarily the most strength intensive job.
Second, Tag skills. When choosing tag skills with Doc Mitchell, the tags would function as a way of keeping the skills you wanted, and the rest would suffer loss. I'm not sure how feasible this is, but I think it sounds balanced. In fact maybe it's as simple as injecting a script at the end of NV's Character creation?
Perhaps a new perk could be granted to the player as well, akin to something like brainless from OWB. In order to give the player one good thing from... getting shot in the head.