I would say that this is more than a fair deal, I have been trying so hard to do swaps for myself, and I'm surprised you got a good of a deal as you did!
If I were you I'd definitely take the WRX, with all those modifications done to it, I reckon it would be a fun car to drive, plus in my opinion the WRX is 100% better than the R.
Either way both ends of the deal would get a good car trade, so definitely trade in the R for the WRX.