Varsovian:
Thank you for your input! Here are some thoughts:
1. I'm considering using NWOD, true. Although the system is closely tied with the whole setting in my mind... But it's true, it would fit - both the main NWOD rules and Hunter: the Vigil. Hmmmm.
2. FATE - eh, not really. I just don't like this system. Too... narrativist, I think.
3. Delta Green is awesome, but it has the same problem as NWOD. The system and the setting are really one thing in my head... plus, the system is quite deadly (on purpose). The same goes for Call of Cthulhu - which I own and like. I'm just not sure if it's right for what I have in mind...
4. Savage Worlds is another system I'm considering. But isn't it too cinematic for a horror game, with the PCs being deliberately favoured by the rules?
Just to expand on the WoD point, it's entirely up to you how much you use. If you just want a basic framework, just go Attributes, Skills and Merits, ignore Morality, Potency and Vitae, and just give out a handful of your favourite abilities with arbitrary 'you can use this once per adventure' limits, and you'll probably be well on your way like that.
Alternatively, you could completely re-write the system, but that would take quite a lot of time on your part!