I use my Magellian on my emulation (w/PowerIcons) AND my peg. sure, the icons that happen to be PNG can't be seen properly, but I don't use Magellian as a workbench replacement. only as a file manager. and I love being able to click anywhere on the screen and have a lister pop up. I've always had my listers use Names - so i can see all the useful info I need (date, size, version, etc).
On my real amiga I used magellian as a Wb replacement, but not being able to really do that now isn't that big a problem. The emulation has alot of memory and so does the peg.
sure, i've had to configure a few things differently, but it's such a useful program, it's worth the (slight) trouble!