Circuit with reverse polarity data lines
Is there a possibility that I create a circuit where it doesnt matter
  which way I connect the the 2 Lines so that one MCU detects which Rail
  is GND and on which rail to send the data?


If you want good data integrity with a single-ended (unbalanced data signal) then you make sure the ground referenced wire is connected to ground at both ends. Having said that, if you want to treat the two (supposedly unmarked or otherwise indistinguishable) wires as swappable and use some electronic circuit to un-muddle the signal and feed the receive MCU the correct polarity then that works but then you get a problem with data sent back in the other direction, like, how the un-muddling circuit will know which way data is being sent so that it doesn't try to do stuff when it shouldn't be doing stuff.

If you are somewhat concerned with data integrity then use a pice of coax and wire it up correctly. Alternatively you can send the signal differentially and use differential manchester encoding because decoding it doesn't depend on which line is which.


  would it be a good idea to implement some kind of twisted pair
  communication?


Shielded/screened twisted pair is probably the best in terms of reducing bit errors and, of course, lends itself to differential manchester encoding/decoding