The main design-related item of note is the sliding piece attached to the bolt that covers the rear of the ejection port when the action is closed. This is Remington's solution for keeping the longer ejection port sealed without lengthening the bolt, receiver, or cycle stroke length. This port cover can sometimes be a source of problems, especially if it's damaged by improper removal or replacement. See
here,
here, and
here for some examples. To be fair, most SuperMag owners don't seem to have issues with their port covers, and even if there is a problem, replacement parts are cheap and the gun can function fine without the cover until you can get them. So if you want to be able to kill your shoulder with 3.5" shells, the port cover shouldn't be a deal-breaker. It's just something to be aware of, and remember to be nice to that part when you're taking the gun apart for cleaning or maintenance.
Also, a lot of the SuperMag's internals like the trigger plate assembly, bolt, slide, action bars, and so on are special parts that are different from those used in standard 12ga 870s. If you're ordering replacement parts or buying them used, make sure you're getting the SuperMag versions of those parts.
On the other hand, if you want to change barrels and use your shotgun for things like slug hunting or home defense, your choices are probably going to be limited to barrels that only have 3" chambers (or maybe even 2.75" chambers, if you're buying on the used market). These barrels will drop onto your gun and function just fine, but don't think your SuperMag receiver will let you shoot 3.5" shells in those barrels. A SuperMag with a 3"-chambered barrel installed can only use 3" or shorter shells, or 2.75" or shorter shells if it's an old non-magnum barrel.
Other minor things include accessories and add-ons. Some aftermarket fore-ends need a bit of tweaking to work on a SuperMag, some aftermarket stocks aren't really meant to handle the recoil produced by 3.5" shells, some saddle-type scope mounts need to have material removed to keep from interfering with the longer ejection port, stuff like that.