You're comparing software-base emulation (of the PS2) to hardware-accelerated emulation (with PeteOGL2), when the PEOPS would be the more accurate compareason (while also still better than PS2's).
Software-based graphic rendering itself does not have the "shortcomings" you mention (you can check so either through usage of the internal soft-renderer or PEOPS)
Which Catalyst drivers do you have? version 8.5 or later are very recommended for a reason...