Can you have 2 junction boxes on one 12/3 cable run
That is fine.  However the junction box must be accessible forever, without disassembling any part of the house, and you must be able to reach the junction box's cover without any tools.  

You don't need to put anything at all (like a receptacle) in the junction box, but you are allowed to if the circuit is allowed to support it.  

Remember -- if you are moving things around, there are certain legal minimum outlets and switches that MUST exist. For instance every point along a wall must be within 6' of a receptacle (along the wall surface, that is).  Every 2' along kitchen counters. Etc.  There must be a switch at certain (expected) locations. Etc.