Since there are so many flavors of Linux, it is tough to make a "Linux" implementation of anything. And since the market is divided, it is hard to pick the distributions. Worse, you have to decide if it will use KDE, GNOME, or some other WM look-and-feel.
Have you tried running Cisco Connect in an emulator like WINE? (I haven't. I'm just wondering)
I no longer purchase devices that require Cisco Connect for this very reason.
If a device doesnt' have a web generic interface (read as compatible with all operating systms), then I blacklist it.
Hard to pick distrubutions? Since most are based off Debian or Fedora, that's really not a valid issue. As for the window manager... they all do the same thing; put windows on your screen with control buttons and menus....