There's no need to worry that upscalers will replace PA -- filtered-upscaled pixel art is worse artistically than pixel art, even if you are not judging by pixel-art's particular standards. The element of distortion and exaggeration in pixel art holds up much worse at larger scales (that is, it is often much better to simply reduce the distortion and exaggeration in order to do a more interesting rendering of details, when you have the pixels to do so.), and there is a general scale problem (when you attain a higher resolution, your eye expects finer details (rather than merely refinement of existing details), which naturally are beyond the ability of the upscaler to produce, since they aren't present in the source material.
I think the only type of graphics upgrade that would not have these downsides would not depend on a real upscaling algo -- rather, it would use a database mapping original graphical blocks (8x8 or 16x16, according to the system) to manually redrawn versions for whatever scale was selected.
(this is fairly hairy video-bandwidth-wise, but we are getting towards having systems powerful enough that that kind of thing could be done in-emulator)
However, there is really such a thing as too chunky -- when each individual pixel gets too big, the overall image stops reading well, and really does look like a mere collection of blocks. On my 20" desktop screen, it's at about 5x for me when the illusion of a coherent image breaks down.
So I do understand the desire to recover something that's more visually coherent from that, even at the cost of some of the finer artistic detail. For sufficiently low-res art on large displays this is a genuine problem.
