It came to me last night while i was sleeping... Its basically a system by which perks that operate in a similar way cause a synergistic effect ... like a tier two bonus...
for example ...
http://fallout.wikia.com/wiki/Strong_Back X3 ranks (using FO2 system) and http://fallout.wikia.com/wiki/Pack_Rat combine to create - Pack mule - Your ability to carry loads is second only to a brahmin. you can now run while over encumbered, so long as you are within 50 lbs of your max carry weight.
or another example is ... http://fallout.wikia.com/wiki/Rad_Regeneration + http://fallout.wikia.com/wiki/Rad_Absorption = Nuclear Powered - Taste the heat, not the meat! From now on, whenever you are suffering from Minor Radiation Poisoning or higher, you can sustain yourself without eating, though drinking regularly is still required.
Now an example of skill synergy ...
Barter 100 + Speech 100 = Silver tongue - You can talk yourself in and out of anything! Seriously... +10% to speech checks and a 10% discount at all shops.
Lastly an example of skill/perk synergy..
Small Guns 50 + http://fallout.wikia.com/wiki/Gunslinger + http://fallout.wikia.com/wiki/Finesse = Pistollero - You are an expert in the use of pistols. +10 damage and +5% accuracy when using a pistol type weapon.
Also, we could also employ a system based on S.P.E.C.I.A.L as well... I have a few ideas about that too...
---------------------------------------------------------------------------
I think this system will help to encourage the use of the cap buy system as well as add far more customization to players. I also think it will be a creative outlet for myself and others coming up with new combination's. There is also a foundation for teir 3 and possible teir 4 bonuses...
New perks to come soon as well ... soon as i think of some ...