Very different products for very different uses. They're built completely different.
Onyx is an excellent option for many shops. It's built for straightforward wide format printing. Excellent support and documentation. It has a lot of wide format features other companies like to charge for (ink calculator, ink savings calibrations, rip/cut, contour nesting, etc).
Print Factory is the ultimate in control of complex outputs, automated color management trickery, analytic data tracking, trick impositions, and more. Hands down the most advanced system in features, automation, and server/client structure. If you like to get into automation or trick print jobs with layers and channel output control, this is the tool to do things others cannot. Another pro of using Print Factory is that their proofing software is very common in ad agencies. Using the same color management math is great for delivering the same output marketers proofed and adjusted in-house.
Over time, Onyx is less expensive and a great option for utility and cost. Print Factory has more power and can bring in more money if you'll leverage specialty jobs.
It's up to your style! I am a trainer for several rip systems, so that's my opinion from a lot of seat time.