I actually might have found a sort of teamwork kind of thing for HM and John.
http://halo.wikia.com/wiki/Spartan_Neural_InterfaceJohn would be able to carry HM wherever he needs to go, like through enemy lines and help him get into electronically isolated vehicles, like tanks. Not only that, if HM and John are combined, it actually increases John's reaction time.
They don't say by how much though.