After reading through the HoR last night there are differences in movement, certain weapon differences, buildings, assaulting from buildings, squad make up (or lack of) and a few other bits that I'm not keen on. The major thing I do like form the HoR rules is the true line of sight needed which I hope is inbuilt into the next edition of 40k.
I like the story line approach to skirmish gaming rather than full campaign capacity. So with being able to buy a couple of guys from here then a couple guys from here doesn't seem to me like any type of squad focus at all. What I do like about the GW kill team rules is you still have a squad approach and get the independence of individual models as a unit. I also like the fact that the rule set is 40k with a couple of additional kill team rules. The HoR is too much to remember entirely and I will being sticking to the GW rule set as for me it's easier and more enjoyable. But hey that's my view and I know a lot of people like the KoH rule set.