I've shot both the S2/S and 645D, including head on on a number of occasions (by using closely matched lenses) and there is no disputing the both the elegant design of the S2/S body as well as it's exquisitely performing lenses. It deserve all the accolades it has received and then some!
With that said there were certain applications where the 645D held it's ground well against the Leica. For close up work in a studio setting and in carefully matching lenses used on each system, such as the Leica and Pentax 120 macro lenses, the resulting files even when examined at 100% were extremely close and hard to tell apart. Same thing could be said for actual close up,macro work at 1:2 (Leica macro only goes to 1:2 whereas the Pentax goes to 1:1)...the resulting files were enar equals of one another.
These similarly produced files ended when the same lenses were used for longer distance shooting. The Leica most definitely had the edge in both central sharpness of the frame and easily bested the Pentax at the sides and edges. Again without looking at the Leica shots in this instance, the Pentax at actual pixels looked really good, but the when the Leica was brought into the equation, there was no comparison and most definitely was superior. Again this was examining files at 100%. Maybe the Pentax 120 macro by going to 1:1 is more optimized for closer range whereby the Leica 120 macro by only going to 1:2 is optimized for mid-distance.
I tried comparing a few other similar focal length lenses between the two systems and again, those Leica lenses are far superior without question but depending how the files are eventually going to be used with regards to output, the Pentax acquaints itself nicely and definitely shows it's superiority in my opinion to higher MP 35mm DSLR's. The newer Pentax 645 optics such as their image stabilized 90mm appears to up the ante in terms of the level of performance. As for support of the system, it's hard to know what Pentax has in store, but they are continuing to bring to market those lenses which have been on the drawing board and more are planned. It's though a very reasonable question and concern though.
The reason I am writing this is there is a lot of varying opinion regarding the 645D and I'm just trying to put it performance vis-a-vis its price range into perspective. If one is willing to do the testing and some leg work as opposed to knowing "out of the box" performance will be perfect (as with the Leica)...a very capable relatively cost effective MFD system can be achieved...and a versatile one at that. The 645D body, although maybe not the most elegant, was well thought out and has some very notable features. Simply it works day in and day out with little muss or fuss.
All great systems including the Hassy's and IQ's...just depends on budget, use and expectations of performance.