I think it would be pretty cool if each pokemon could have one HM spot.  What I mean is aside from the four moves it may learn, it should have one slot only for HM's.  The HM could not be removed or changed once placed in there and could only be used outside of battle.  If you want to give a pokemon two HM's then you would have to sacrifice one of regular four move slots for the seond HM and this one could be used in battle. 

I'm sure pesky HM's have ruined some great storyline teams and when you're toward the end of the storyline, an HM slave sacrifices a slot for powerful team of six.

Just a suggestion...