I think that reputation right now is rather useless statistic. The only real advantage you can get for having high reputation is Gunrunners thingy. Other "factions" doesn't give you anything for being "loyal" to them... And reputation drops if it is higher than 200 (or lower than -200), so you have to work hard to gain it. If there are no quest for rep gain, then it's almost impossible to have high reputation at NPC factions.
So my suggestion is:
- Make less factions. It's rather useless to have 3 different reputations for residents of the same city (for example BH ghouls, humans and mutants)
- Reputation shouldn't change over time. You should live with your high/low rep OR reset it at cathedral.
- There should be a way to upgrade your rep up to 0 in each city. You would pay, let's say 1000 caps per 100 reputation gain.
- High reputation should give you some small advantage, similar to Gunrunners workbench (for example: access to special merchant, no need for Day Pass in VC, access to higher quality slaves at Metzger, cheaper blueprints etc.)
- while your reputation wouldn't change over time, at the same time it should be slightly harder to gain high rep.