If I understand you correctly, you're saying that more sophisticated malware with keylogging isn't slowed down at all by good key stretching, and such sophisticated malware has become fairly commonplace. I couldn't agree more...
Good key stretching is still important if you ever intend to keep wallet backups stored anywhere online (e.g. a backup services), and it can help protect against stupid malware (which still exists), but I agree it does nothing against sophisticated malware. In short: good password key stretching can sometimes help, and there's no reason for any wallet software to use weak key stretching (except of course that it requires development effort, and developers have limited time and long lists of new features to be added).