As someone that lives and plays in higher altitudes of the Rockies, there is no question there is significant power loss as a result of (less Oxygen) high altitude in most engines. From snowmobiles, ATV's to boat motors, they all struggle in the rarefied air. My former RZR had the exact same issue when we were on high mountain trails 8500' to 10,500' or higher. Yes, more CC's would help, but the only thing I know that really helps to compensate for high altitude is a turbo. However, turbo's can create reliability issues and are very expensive. I have taken my P-4 to the top of mountains, and yes, it did lack power at the highest altitudes, but it had enough bottom end torque that it made it up anything I needed it to. For 95% of the owners that won't be riding above 9000', on a regular basis, the Pioneer power plant is just fine. For those riding at high altitude and needing a UTV for hard work and steep challenging terrain, the Polaris 900 XP or 1000 CanAm will offer more deliverable power at the higher altitudes. Then again, they cost $3000 to $4000 more (equally equipped).
I have also noticed my P 4 is getting a little more powerful as it breaks in; not by much, but it does seem to pull a little quicker than when I first got it.