I've been doing crossfit now for about 3 years on and off and CrossFit Endurance is a new protocol based on the Crossfit underpinnings (olympic lifting, pullups, sprinting, rowing, running, and gymnastics at high intensity and variety). The idea that the CFE team is proposing is that LSD (long slow distance) training mostly leads to overtrained endurance athletes. The team have taken POSE running technique from Romanov, added high intensity, highly variable interval training and put it on top of a base of standard Crossfit training. The premise is that by cutting out up to 75% of the training time, endurance athletes can get better results by using the remaining time to work on short-burst anaerobic activity which it turns out benefits your aerobic capacity directly.
I took a 2 day certification with Brian MacKenzie (the primary founder of Crossfit Endurance - not Crossfit) and learned a lot. They're still working on proving out the theory at an Olympic level and that could take a few years.
Anecdotally, I know that my Crossfit base (without the CFE interval work on top) benefitted my trail-running immensely. The heavy lifting, seeming ability to clear lactic acid quickly, and just general mental toughness that you acquire from the training all boosted my trail-running and mountain biking capabilities, even though I wasn't training in those sports. I've just started adding in the CF/E interval workouts so that I could do some triathlons so it's too early to tell the overall difference. I know that my running style is getting more efficient and my running pace is increasing.
I don't know much about P90x but seem to hear good things about it here on RJ. I'd say, try both, and see what you think about them. I love the camaraderie, and the community inside Crossfit and to me, that's at least half of the joy of that protocol for me.
BTW, I just did my third Olympic triathlon in 11 weeks and I've been training almost exclusively with Crossfit and CF/E workouts and very little long slow distance training.
You can learn more at these two sites, neither of which I'm affiliated with (other than as a Level 1 certified coach in CFE, but not in CF yet.)http://www.crossfit.comhttp://www.crossfitendurance.com
Also, I wouldn't say "which is better", I'd start with your goals, then figure out which would better suit your goals. Since you're trying to address running injuries, I'd certainly point you towards CFE since it's really been designed to address exactly that issue - lowering training time, improving results, and decreasing injuries through better footwear choices (flat / no support shoes like Innov8 or Adidas Adizero RC or many others), better and more efficient running gait (like POSE or Chi Running), and less time on your feet (in each stride and in your life.)