With the canon 6d / nikon d600 being in the $2,000 ballpark, can we expect the entire aps-c size sensors to slowly disappear as the whole idea was to make a DSLR cost effective ?
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Yes, the 650D is a decent step up from the 500D/550D/600D in terms of AF for stills. The previous recent xxxD bodies have 9 points, only the center is a cross-type, and it's a single 'hybrid' cross, with one f/5.6 line and one f/2.8 line in a '+' shape, while the outer points are f/5.6 lines. The 650D inherits the 60D's phase AF - still 9 points, but the center point is a dual cross, an f/5.6 '+' with an f/2.8 'x' superimposed, and the outer points are all f/5.6 crosses. The f/2.8 lines are more accurate, because they have a wider baseline.
However, I should point out that the better AF itself may not solve the problem for your f/1.4 primes, for two reasons. First, the xxxD bodies don't offer AF microadjustment (neither does the 60D, although the 50D does, else it's 7D and up). AFMA is especially important for fast primes, where the DoF is thin. Without AFMA, the only option for a front- or backfocusing lens is to send lens(es), and possibly body, to Canon. Second, even with a perfectly calibrated lens, shooting a fast lens wide open using focus-recompose basically guarantees you a backfocused shot, due to geometry. So, if a new 650D plays nice with your lenses (or you're willing to send to Canon), and if you use those outer cross-type points to AF, instead of focus-recompose from the center, then you should see sharp focus (as sharp as possible, at any rate - do keep in mind that lenses aren't at their sharpest wide open).
Hope that helps...