> No decent office suite
StarOffice met my needs just fine; I could get work done in it, and it supported more Word formats than the latest Word (with occasional breakage - but that was rare).
> lack of support for many soundcards and modems
I think this was the case, yeah. You still had to be picking your HW to be Linux compatible (as opposed to these days where it's just a good idea).
> severe distro / package format fragmentation wars
I think much of that started later; at least, insofar as it impacted me. My experience was RPM pretty much dominating at that time.
> Lack of staples like Flash.
I don't recall what the flash situation was; on the other hand, that probably means it either worked for me[1] or I wasn't noticing the lack of it which would imply it was less of a staple.
[1] admittedly, this would undermine my initial point, as the question was really "a completely free-software desktop" not "a linux desktop", but I honestly can't remember.
> Instant messenger clients didn't support all features that the Windows versions did.
This is true, but it's hardly the difference between "car" and "no car" - more like a car with or without a CD player or something.
> No gaming to speak of.
I've played a lot of great games on Linux which were available then - I still go back to nethack from time to time. Admittedly, first-run commercial games weren't being released under a free license, but given Stallman's comments elsewhere that may be tolerable. There were some near-first-run games (and you weren't buying enough of them! 2001 is when Loki filed for bankruptcy) and Id was in the practice of releasing their games for Linux right away (and GPLing the whole thing years later).
> it was only practical to use on the desktop as part of a dual boot.
I wasn't dual-booting at that time, and it was practical for me.
There were certainly things that might have demanded Windows (there still are a couple, although I think virtualization is slightly more in vogue than dual booting?), but most people didn't need them like they need their car - remember, that's what I was responding to.
If you want to say a free desktop was like an ugly car you had to get up on blocks fairly often and source your own parts for, I'm much more on board.