The cost may not be as much as you think. If I have a quality modded Gen 2 (Ohlins, Brembo Brakes, wheels etc.) I'm not going to get much value for those things if I trade the bike to a dealer or on the resale market. Going to the Gen 3 would cost about $10-11K. The main difference between the Gen 2 & 3 is the QS, TC, and ABS. I can add that for about $2,500 with something like a Gripone, but like you say it won't be integrated and I don't have any expansion.
So if I have a development plan for the Gen 2 like adding this first, getting the kinks worked out, then later stepping up the motor it's just not that big of a reach to pay $5k for it. And I can do what I want with the tuning, no waiting for a magic hack. All in all, this is the cheapest way by far to a high-power, full-featured Busa.
A pretty interesting alternative here. Would you provide it with a flashed ECU map and all or would I have to get the ECU and map it myself?