I didn't want to bloat the OP so I decided it'd be best to directly insult shaderfags in a separate post.
>upscaling and anti-aliasing, and that can't be done with pixel based stuff.
You can upscale pixel based stuff. What you're thinking of regarding making 3D look less aliased is increasing the internal resolution. This does benefit some 2D games, with certain emulators allowing for higher resolution rendering of Mode 7 effects.