Just to add in what happened with TwistysCash - yes we went to v4 and then went back to v3.
We didn't do it because v4 sucked or didn't work, or was too slow or anything like that at all. We did it because of the same reasons as Selena and a lot of other people in this post are referring to: It's a little too different from v3.
We have been running nats3 for a long time and have not only been happy with it, but we've also built our business processes, management systems, pricing options, customer support, basically EVERYTHING around Nats3
Doing the upgrade from v3 to v4, we thought our existing business processes etc could have been easily imported into v4 - that was not the case at all and we had to roll back. We're going to regroup and try a more gradual approach so we can change our business processes so they will work smoothly with Nats4.
Nats4 has way better stats, better control, better security and way better tools for affiliates - although as Nurgle and others point out, they're not totally user friendly yet ;) We definitely want to take advantage of these improvements, we'll just have to go about it in a different manner.
So! To answer your question Jact in the most long-winded way possible
I believe setting up your program in Nats4 to begin with is the better route to go. You will have made your business processes based on a more robust system without have to revisit them at a later date if you did it on Nats3
Hope that helps!