MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
UPDATE: SEE MY POST ABOVE FOR MORE DETAILED PRINT INSTRUCTIONS.
Try ABS. I found that PLA is too brittle for many of the parts that need to bend (it's okay for the ball part of the joints, though).
If the ABS is still giving you trouble, it's probably because you are getting poor layer adhesion; for my ABS I am printing at 240 with a fan speed of 40% on the i3 mk2s.
I'd also recommend experimenting before you do the whole print. Start with either the lower leg and foot, or with the forearm and hand. Those are the pieces most likely to break if the piece is too brittle, or if you're getting poor layer adhesion.
I haven't tried with a high-strength PLA like Polymax or Tough PLA, but I have some Polymax on the way; will experiment with that to see the results.