First of all, just because Origins is written out due to DOFP, there are still logistical issues in Deadpool. In XOW Wade Wilson's mutant ability is agility. However in Deadpool he is a human, as Ajax says that the serum/expirements will bring out any X-genes hiding in his DNA. If he already has a mutant ability, then Ajax's expirements shouldn't have given him healing powers.
Perhaps Wade Wilson doesn't have mutant agility powers, he just has great human agility in Origins? Or perhaps the expirements triggered a second mutation?