I think the 92/93 Milan team was better than the team of the following year. The 93/94 outfit won a mere two out of six in the group stage, despite having average opponents (Anderlecht, Werder Bremen and a Porto that was dissatisfied enough with its coach, Tomislav Ivic, that they allowed him to leave after the group stage ended - replacing him with Bobby Robson).
That performance against Barca still confounds me. Mind, when I looked at Barca 93/94's record in Europe, they were almost eliminated at the first hurdle by Dynamo Kiev. Their vists to Istanbul and Moscow in the group stage ended in draws. In other words, once they hit the road they weren't as impressive as one would expect a team boasting peak Romario and peak Stoichkov to be.
There was basically a change in the core in Milan in that season 92/93 to 93/94.
The 3 foreigners were swapped out (Van Basten, Rijkaard, Papin out - Savicevic, Boban, Desailly in).
They gave up on the great Italian hope in Lentini (who would never fullfill his fantastic potential, not really) and the defense stayed largely the same (Maldini, Baresi, Costacurta and then Tassoti replaced by Panucci).
They were brilliant, pragmatic and tight defensively... A CL win in 1994 and the final appearance in 1995, but the X factor offensively was always Savicevic.
Boban, Albertini, Donadoni and Desailly was the go-to midfield that played narrow and they dominated with and without the ball (if that makes sense... they were comfortable without the ball, and then they transitioned brilliantly forward).
Massaro was up-front and he was always... Adequate. But he was never the player to make the difference on his own.
And after they brought in Savicevic, it still worked. But with no more MvB, if Savicevic wasn't there, they were offensively somewhat challenged. Simone and Massaro, while servicable, and far from "bad players" were not really the class to make a difference on their own.
And that's what happened vs Ajax.
To this day, we don't know if Savicevic was injured or just in a row with Cappello (he said he was fit, Cappello said he was injured).
Him (Savicevic) and Boban had a wonderful tie vs PSG in the semis, winning it for Milan... And then no Savicevic in the final.
Without him, Milan put up a decent fight - but you always had a feeling Ajax were going to score first if there was a goal.
But I do agree that Ajax squad was special, even without Seedorf the following year.
So, I'd put forth the following three teams (losing finalists 3 years in a row, though 2 of them won in before losing the following year):
93/94 Barca
94/95 AC Milan
95/96 Ajax
I think 1997 Juve is in with a shout as well... I'd say 8 times out of 10 they beat that BVB team, but it was one of those nights.
Deschamps, Jugovic, Zidane, Del Piero, Boksic, Vieri.. They were packed. Things just didn't go their way that day.
I don't know why exactly, I cannot put my finger on it, but that period might be my favorite in CL history for some reason, 93-97.
Next few years we got Real winning it 3 times, Valencia and Bayern there... I don't know why, it didn't feel as special, it was like the great generations of certain clubs got scattered and outside of the Man Utd / Bayern final I can't say any of them stick out to me.