Because we do it better than machines, and on a case-by-case basis. More sharpness there, more definition there, more blur there, whatever. It's not just masochism.
Though arguably most of that would be achieved as well by a combination of auto-aa, masking of the layer holding the auto-aaed version, and blurring, with a little touchup, depending on image scale. I've experimented with that successfully. The main value in doing it manually is better artistic flow (by which i mean mental flow), say I.
I just tried it again, and agree with the above still. The obstacle is mainly, when you apply AA yourself, you're working forwards (adding to the picture). When you're reversing AA, you're working backwards (removing what's been added)
also some of the AA algorithms out there are a bit sketchy
Really? I thought it was pretty simple for most kinds of AA.. just 'how much of this sub-pixel triangle falls into this pixel?' (which can be done by basic arithmetic). The only AA sketchiness i've seen is quantization (only, say, 16 levels of AA). Which wouldn't normally effect pixel art. Do you have any examples?
MsPaint: '640k should be enough for anyone' should summarize why it's a bad app. It's bezier tool is okay IIRC, okay enough to warrant 3 points.