Emir,
The main benefit you would see is the smoothness of the Rupes. As far as speed of correction, I think they are both on fairly common ground. The slight edge might go to the Flex. I have both and I like both. I like using the Rupes when I am not working on a car that is in bad shape. It barely has any vibration and will not walk you across a panel like the Flex will! The only other thing the Rupes might have a slight edge in is finishing but I am just basing that on things I've read not not an actual comparison of my results.
All that said, I don't think there's anything major for you to gain here unless you have trouble with the Flex or do not like the difficulty of control. It would be hard for me to pick one though if I could only have one. They are both great polishers. Flex is sort of like Dirty Harry, he will knock it out quick, but the process can be violent. Where the Rupes is like James Bond. A little smoother and more refined, but able to take on just about anything just the same.
Just on a side note- You said you would have to get new pads for the Cyclo, but you still would for the Rupes if you are using 7 inch pads with your 3401 VRG.