Fundamental to most peoples complaints about desktop Linux applications is the lack of look and feel cohesion across all permutations of distro, desktop, and toolkit.
Wine applications using the Windows APIs look like complete garbage and fit in nowhere. The same would be true of OSX Cocoa apps - they wouldn't mesh well at all, and it would be practically impossible to skin them with toolkit theming.
That, and recent efforts by Gnome and KDE have been producing tons of good new applications with modern GUI. They just aren't all the applications yet.