Today a patch was released for the PC version of Sonic 4 Episode 2, now anti-aliasing works for any 16:9 resolution. It even works with custom resolutions, like 640x360, 800x450, 1440x810, 1680x945 (these custom resolutions can be used by editing the UserConfig.cfg file with a notepad, these should be used only in the window mode though), as long as the resolution is 16:9, anti-aliasing should work fine (the following link has a guide on how to force anti-aliasing).
http://forums.sega.com/showthread.php?411178-PC-Version-Sonic-4-and-Anti-AliasingHere are a few 1920x1080 comparison pictures.
Before the patch:
http://cloud.steampowered.com/ugc/542930348506325084/8472AF3B9C68EBBD9D6EDDDB819E77A1AC0FF750/After the patch:
http://cloud-2.steampowered.com/ugc/542930348506224720/315EEA7FC731810A41C65EEF46721DDC045746B6/After the patch with 8xMSAA forced through the graphics drivers:
http://cloud-2.steampowered.com/ugc/542930348506275314/32CFDE2ECBDB01E36D3C8D27DA5211F47545B94C/I would have also taken a picture with SSAA, but I don't have a 1920x1080 monitor, the pictures were taken in my brother's PC (his card can only force MSAA through the drivers, there's no option for SSAA).
Other than the image quality improvements, the patch also improved performance at lower resolutions.
This was tested in my almost 6 years old laptop, with a Core 2 Duo T7200 (2.0GHz) and a Mobility Radeon X1600, in the early part of Sylvania Castle Act 1:
1280x720 Before the patch - 20~25fps
1280x720 After the patch - 20~25fps
640x480 Before the patch - 25~30fps
640x480 After the patch - 45~50fps
800x450 (custom resolution) Before the patch - 25~30fps
800x450 (custom resolution) After the patch - 45~55fps
640x360 (custom resolution) Before the patch - 25~35fps
640x360 (custom resolution) After the patch - 60fps (with a few rare minor drops)