Since this discussion seems to be still up to date...
Why not simply override the rendering settings for matlab in the graphics driver?
Using my nVidia card i simply start the nVidia control center, add matlab.exe as a
program using custom settings and choose "Override all application settings" (i hope this translation from my german graphics driver is correct) and set
Antialiasing-transparency = Supersampling
Antialiasing-setting = 4 or 8 or ....
I cannot tell if it works well with everything you can plot in matlab - but so far it does.
I'll see when I find the time to look into it.
Something else I just noticed: Using plotyy and setting both y-labels, title, xlabel etc and tightfig. to wrap things up. Tightfig seems to fast somehow. It messes up the figure window. It works if I include a pause(0.2) before tightfig. Strange..... but the workaround is no problem of course.