I have several Hasselblad bodies and lenses and have previously owned two SL66 cameras. They are both really excellent systems, the build quality for both is just great. The Zeiss lenses are essentially the same (the SL66 lenses lacking, of course, the leaf shutters that the Hasselblad versions include. And I'm assuming here that you're interested in a Hasselblad such as the 500C/M and not one of the focal plane shutter bodies). If you're okay with the focal plane shutter of the SL66, it's kinda nice not to have shutters in every lens (that need occasional servicing). And the SL66 does have some interesting features that you won't get with the Hasselblad, notably the built-in capability to reverse the lens mounting (combined with the bellows focusing this allows pretty extreme close-ups even before resorting to any extension tubes) and the lens tilt (allowing you to extend focus along a plane without having to rely on smaller apertures). Of course you can add a bellows extension accessory to the Hasselblad for great closeup work, but the SL66 is cool for its included capabilities in this area.
Also, the SL66 film magazines have a switch so the same back can be used for either 120 or 220 film.
Things to consider regarding the SL66: the bellows focusing, as with any camera that uses one, is something to be a bit careful with (as in, not poking holes in the bellows during handling). Also, the SL66 is a little bit larger and, with the bellows focusing, a different handling camera compared with the Hasselblad for handheld work. If you plan to use mostly or exclusively on a tripod, no problem.
At any given time there are many more Hasselblad bodies, lenses, and accessories available in the market (especially lately it seems) than SL66 items. So for sheer availability the Hasselblad route is bountiful, to say the least.
Of course, each camera system out there has certain definable features which can be listed and evaluated... and then there is the intangible, less well-defined "feel" and such that only handling the things can let you know which you will want to keep and actually use. I really liked and appreciated much about the SL66. But, as I mentioned, I have lots of Hasselblad stuff today and no SL66. I just didn't find that I often used, for example, the lens tilt feature (even as cool as it is). And for more casual, handheld stuff I like the compactness of, say, the 500C or C/M with the basic 80mm Planar (or 60mm Distagon). For a 6x6 camera with interchangeable lenses and film backs, they made it about as small as they could! It works for me.
Good luck with whichever you decide upon. Like I said, they're both superb.