The Hy6, in my opinion, has better ergonomics and a much better battery system. The stock 6008AF batteries are pretty terrible, at least by this point in time. Sometimes, particularly in the cold (maybe not a problem for you unless you come home!), the batteries will only work for a single roll on a full charge, particularly if you have let them sit for a few days. So unless you replace the batteries with fresh packs and use a new style charger, your 6008AF experience will be one in battery management. The 6008AF also shuts itself off rather quickly, because of the battery issue, so often when you come back to the camera, you will need to wake it up...it will make a small noise and be ready to shoot in less than a second, but it is still a little annoying.
The Hy6 uses newer lithium batteries, and they are just standard camcorder style batteries, so they should not be hard to find or replace.
Overall, the Hy6 is lighter and more refined to use, though the body shape is a bit strange (quite long compared to most cameras!). The release is more refined...the Hy6 has a nice large button that has some tactile feedback. The green plastic release on my 6008AF was pretty finicky. It required a very light touch for the half-press, and just the tiniest bit more pressure would trigger the release. Even after using it for years, I would still occasionally have misfires. The shutter and film winding are LOUD. The loudest of any camera I have owned. Loud enough to make subjects jump the first time they hear it, and I took to warning people. The Hy6 is much quieter and better damped.
I did not find either camera to be particularly good with AF, though I would give the edge to the Hy6. The S2 blows them both away in this regard, as the D3 blows away the S2! Even if you want to use AF, I would consider investing in a split-image microprism screen, just so you have quick visual confirmation on what is being focused upon.
Despite the annoyances, I would probably still recommend the 6008AF, especially if the money is an issue. But only for film use! Despite all I say above, it is a very charming camera to work with. I think the film magazine design for the 6x6 back is better than the backs designed for the Hy6. They are bigger, but they are quick to load and the long straight film path leads to sharp results. I got sharper results on my 6008AF than I did on my Hasselblad, even though the lenses were often the same (110/2 Planar for example). The viewfinder is superb in both cameras, particularly with the waist-level finder. I liked the look and overall tactile feedback of the 6008AF better than I did the Hy6. The Hy6 is easier to shoot handheld, but the 6008 has actual shutter speed rings and aperture rings...the Hy6 did away with that. It is certainly better looking to me than the Hy6, but that's simply taste!
One caveat would be that if you are going to require AF, the 6008AF will require you have AF lenses with aperture rings. They dropped those lenses later in the production, which was a real poor decision in my mind. So if you are looking for all AF lenses, it might be easier with the Hy6.
I have never used 6x6 on the Hy6...I sold mine before they came out with the back....I waited for years, finally got fed up and sold it all and moved to the S2 and stuck with the Hasselblad for a film MF-SLR. I know I will have detractors for saying this, but I would avoid both for digital use! I think the systems that were built from the ground up for digital like the S2 are just light-years better. I had the Hy6 with the e54LV 22mp back, which is admittedly old, but it was not even in the same century as the S2 in results, handling or lens performance. Given that S2's are now being sold under 10,000 dollars, I think if digital is in your future, better to consider that route. Keep film cameras for shooting film, and digital cameras for shooting digital. The hybrid solutions are not particularly effective, at least not in my experience.