Good question.
I shoot USP's better than any other handgun, so if we're going for actual USE, I'd probably take that one. However, that's just me, so it's not really applicable to anyone else.
Here's my comparison... bear in mind that I am not going to compare the actual handguns since there are as many people that would say that a USP is better as would say that a SiG is better.
Price: On average, the USP9SD is about $150-200 less expensive than the SiG P226R Tactical
Sights: USP9SD has elevated, adjustable sights while the SiG has night sights. My nod here goes to the SiG. With night sights and both-eyes-open shooting, you don't really need the elevated sights. The HK sights are all black - no dots or anything. I didn't like that. The USP9SD sights would be the first thing I'd change on this gun - I'd want night sights.
Barrel: Both have a 13.5X1LH thread pitch. The USP9SD gets the nod here because it comes with a thread protector; the SiG doesn't.
Gun case: The SiG comes with the same Blue case you get with any other SiG. The USP9SD comes with the nice black zippered case with the pouches that can be rearranged (velcro), cleaning kit and even a suppressor and accessor pouch. Nod to the HK USP9SD here.
Magazines: Both come with two factory 15rd mags.
Rails: HK uses their proprietary rail (yes, you can get adapters, but they are a bit awkward)... SiG uses a standard rail. Nod definitely goes to SiG.
My take is that the SiG is the better gun given the rail and sights, but only if it's worth an extra $200 to you. It should be noted as well that the SiG is apparently limited to only 300 made. SiG doesn't sell the threaded barrel except with this gun.
If I could only buy one of them, I'd go with the USP - and then buy new sights for it.