Hmm....

If we make THF as a branch from ROG, the main thing would really be establishing some sort of specialization for THF so that it stands out from NIN. For that, I'd suggest the buff to Throwing Dagger go to NIN (make it generate Ninki or something), while buffing Mug for THF. This is merely thematic, but I feel it would fit both jobs while also being callbacks to older FF games (where NIN's main gimmicks were Dual Wield and the Throw command). By the same token, Sneak Attack making a return as a THF-only skill would be a step in the right direction, specially since you have the Stealth Gauge.

I'm looking over your OP so that I can give better feedback, but there are some good foundation in there.