Wyrdwars is an ongoing development of Coreheim which was a fan based clean up of Mordheim. Wyrdwars seems to go further towards levelling the warbands and fixing some of the problems a lot of people see with the original GW game and the poorly tested way it developed past the initial release.
Both sets are free, Wyrdwars is all together in on place while Mordheim is a bit of a web-archive hunt to get all the expansion bits together, the warbands are virtually identical so figure choice is pretty much the same either way.
Personally I am an original Mordheim fan so my biased suggestion would be to go with the original. That said Coreheim or Wyrdwars deserve support for the enthusiasm that is behind them and the quality of what has been produced (and huge kudos for keeping the game going after GW dropped it).