Registration, IMO, is for the purpose of showing or to help sell your horse.
If I had to choose only one it would be AMHR because there are no AMHA shows anywhere in Wisconsin (personal gripe).
However, if you want to keep all your avenues for selling horses open you need to have them in both registeries as other parts of the country (I've heard Kansas) has no AMHR shows.
My horses are all triple registered AMHR, AMHA, PtHA (because I have shown Pinto). As for the WMCMHR, I hear so little about them and have never seen any shows by them so I don't even consider that registration worth the paper it's printed on.