The only real problem for me was that 2nd ed's profciency/skill check system was such a mess, which made psionics so troublesome and thus, impacted on Dark Sun.
If we'd have had 4th ed's skills and Skill Challenges back then, wow!
Played several campaigns in Athas as DM, awesome fun

currently on 4th ed homebrew Dark Sun.
The flip books were a great idea, as until then the way adventures were written/laid out was still horrible, the 1st ed module layout was absolutely bloody atrocious to work with: dense blocks of text, with little refference etc. Ugh! So, the flip books were a cool attempt at a better way, it was much better but still not as good as late 3.5 and now 4th ed layouts
Artwork, sorry, blows pants out of 4th ed. PhB3 and now Dark Sun are the only cover art for 4th ed I really like (good artists, I just really don't like the 4th ed style of art, it just doesn't "grab" me, like Brom, Caldwell, Parkison and Easley do/did,
damn those guys were frikkin' awesome!!)
Half-giants were
kind of broken...but everyone knew that their Wisdom sucked, so, do you want a charmed half-giant with the damage output and toughness of a Tiger Tank on
your team?

Thri-kreen couldn't wear armour....so got pasted, a lot.
Thus, both in the end, were not that over balanced.
I made my own rules for psionics to help with the issues back then
http://www.silverblades-suitcase.com/adnd/htm/print.htm
character trees were VERY helpful. the setting was brutal, which I relaly liked (even though I usually like very heroic romantic adventure like Spelljammer). But I was lucky in that most of my players knew that Athas should be nasty, and respected it, and knew to always have "Escape Plan B" prepared:
RUN LIKE FUN!
I abhorred the way the setting got changed so always kept it to the original boxed set (Tyr becoming a democracy?! oh get knotted!

)
The entire way it became a struggle for survival, where "dirty deeds done dirt cheap", was the norm, was awesome. back then I was reading the "Thieves World" books, so it all fitted in nicely
By the way, the computer games were available for
legitimate download, iirc, but I don't know about now? I have two of the collection boxed sets, but for Amiga! lol
I dont' care what folk think, it was NOT having too many settings that caused problems for TSR...it was TSR's issues internally actually, because as a D&D player I likee others, had lots of choice to BUY and did so because the stuff was bloody brilliant!
