It depends some on your application. Isn't the Dart a racecar? If so, do you plan to race the truck or just drive it?
Personally I think the 6.4 with VVT and SRV is the better all around option. More bottom end without losing top end. But...they have weaker pistons and should be swapped if you plan to boost it or anything. So take that into consideration if you plan to turn it up in the future. Personally, I would delete MDS even with the 8HP. That's the one thing I don't trust on them.
I think the 6.1 is a little more robust and things like cam's are cheaper. And they can certainly be built to be equal to a 6.4. Plus they are simpler since they don't have VVT, not that I have heard of anyone having issues with VVT ever, and they never had MDS. Pretty sure you could run the 6.4 intake on the 6.1 if you wanted to add the SRV functionality though.
I've never owned either, but based on my understanding I would say a 6.1 would feel like a build SB, a little more peaky and softer at the bottom but very fun. The 6.4 would probably feel more like a good BB, just bigger everywhere.
Also, what has you turning away from the Dart?