Personally I'd then like to be able to use that in subsequent playthroughs to experience other storylines and arcs. There would be a lot of stipulation regarding levelling etc, for example, any skill books taken in previous playthroughs shouldn't spawn in subsequent ones. Implants would remain, but if you've maxed them in one playthrough, you're still restricted by END so can't get anymore. That kind of thing. With New Game + you shouldn't be able to achieve a build that isn't possible in a single playthrough, you just have the benefit of using a character from the start.
In terms of equipment I would also suggest restrictions on what gets carried over. Maybe have a screen similar to a vendor when you start a New Game +, with weight restrictions, and number restrictions on weightless items (such as Stimpacks, and even Ammo), thus not allowing you to start with an extreme amount of high level equipment, but enough for your character to still use his/her specialised equipment (for example, I'm currently level 16 using a Reinforced Leather Armour, Pre-War Hat, Combat Knife, Hunting Rifle, and .44 Magnum). Also, a Bottlecap reset so you don't start off filthy rich.
Anyway, that's a brief overview of my take on the system, and possible balancing issues. Any further thoughts, suggestions, and opinions are most welcome. Thank you for your time!
