i had the very same dilema before buying a kit. I got a Magic Pie in the end but was not impressed by the hill climbing, my rear motor will die on steep hills without pedalling. I now have front and rear pies connected to one battery and the difference is unbelievable.
I have not tried the 48v/1000w motor so I cannot really comment. Build wise the HBS 1000w will be a little lighter but the power cable will come out of the axle and not the hub as in the MP. there is the choice of the internal controller on the MP if you want to build a neat discrete bike. The HBS 1000 is probably a little quieter and I believe it to be faster. I did read somewhere that someone had tried both and the 1000 HBS was faster and better on hills than his friends MP??
I have tried looking at the pdf performance files on GM's website in the hub motor section and i'm sure the 1000w HBS has a better torque performance?? try looking yourself. On the motor comparison page it gives the torque/power figures for all the motors apart from the MP which just says "coming soon", Hmmmm.....
If you can afford it get two pies and wire to one battery