I like the fact that the BMW rack is low profile (at least on the K12R. Would assume its the same on the S). The HB rack seems obtrusive and makes the bike look like parts are missing when the bags are off. Might be a trade-off for security, but I've had my R up to 125mph w/ loaded bags and didn't have a problem (yeah, not a good idea, but the opportunity presented itself).
I had HB bags on my Guzzi and they were not nearly as good as the OEM bmw bags. Big plastic jellybeans that did nothing for the aesthetics of the bike. All bags leaked, but mine seemed to leak and pick up mold. I opted for the 'smaller' bags that wouldn't fit a helmet. Had I gone for the larger bags (40 liter? maybe 30 liter - don't recall) that did fit a helmet, I would have had to widen my garage door. I suppose a top case is an option, but the HB topcases are only slightly uglier than the Givi topcases.
I like the fact that the beemer bags are keyed to the bike. I don't know if that's something that HB offers now, but it wasn't an option for my old bike. That meant one key was slowly wearing a circle in the dash-plate as I drove down the road. And, god help you if you lose your HB key.