According to the reviews online, both colleges have their own pros and cons, and here are some comparison points which might help you make an informed decision.

• The location of both the colleges are good, be it Gandhinagar or Dehradun.
• The UPES campus is much bigger compared to the PDPU campus. But both are well maintained and facilitated.
• PDPU provides B.Tech in Petroleum Engineering while UPES provides the same in Applied Petroleum Engineering. The former is considered to be far better and more advantageous than the latter. 
• Curriculum of PDPU is very well prepared encompassing all major aspects. It has now been bifurcated into upstream and downstream.
• Placements at PDPU are much better compared to UPES.
• PDPU is visited by core companies like ONGC but UPES is mostly famous for its relevance among IT companies like Accenture, Wipro, etc.

Lastly, it can be seen that PDPU, even being a newer institution has grown a lot compared to other colleges. They are visited by core companies which hire students offering them a salary package of 14-15 LPA. So, it will be better if you go for PDPU as it will give you proper industrial exposure and opportunities.