I've always felt the Jazz biggest flaw was bad timing. They peaked (the two finals years) later than you would've thought given the age of the team. Granted, I thought we should've been able to beat Chicago the second time, and that long layoff after we disposed of the Lakers didn't help us like many thought it would given our age...in fact, I think it disrupted our rhythm. The first finals team really pushed the Bulls hard..given the respective circumstances, I thought we were better in that series than the second one.
The '99 team started out gangbusters and definitely got worn out by the condensed schedule and often times the back-to-back-to-back games, while the Spurs started slow and then got white hot and overtook us for that 1 seed via tiebreaker. Once we lost that I knew we wouldn't get out of the west, and that was the beginning of the Spurs dominant stretch over us (and Portland too for awhile).
Other than that, as many will agree, '95 was really the biggest missed opportunity. Sure the Rockets beat everyone else too and in dramatic fashion also against PHX but I felt we choked in that series as opposed to them really being better than us (they were the yr prior). Had we beaten them I liked our chances to get out of the west and beat Orlando in the finals.