It depends on your budget and your research (research/diagnostic). I prefer Rotor-based machine for daily use, (research only not for diagnostic use). It easy to use, very flexible and easier to get the reagent/chemicals since most of the Rotor-based doesn't need very specific requirement.
I will suggest that you decide this depending upon your work preferences and budget.
As suggested by Michael Hornsey, Peltier element-based thermocyclers are generally more versatile. Thus if you have the work based on these types of qPCR you can definitely buy this.
Yes, this depending your work and budget . The qPCR instrument isn’t inexpensive, and you’re going to be using it for years to come. For that, make sure the system works for your application, as well as applications support and training that you need for today and in the future.