Ok, let's break this down:
MBX5 is the older buggy. It has plastic chassis braces (plastic ends with a metal turnbuckle-type link in it)
MBX5 ProSpec has metal chassis braces. It is the "higher end" version of the regular MBX5. There is no performance difference really... in fact I (and a lot of folks) ran the "standard" plastic front chassis brace on the MBX5 ProSpec to allow a little more chassis flex for better cornering.
MBX5R is an updated version: It has a lot of minor changes, but the major changes are taller shock towers, longer shocks with screw-on bottoms instead of clips to hold the seals in, a different ackerman plate, a different front hinge pin holder, different upper arms with "hump" in them to allow more suspension travel, and knuckles that allow more steering throw. The MBX5R turns better than the MBX5/MBX5 ProSpec. It has more suspension travel for more droop also.
All 3 are great buggies.