My shoddy memory says you are right, that it looked like the better team losing both times, but I think that was more down to expectations and personnel. In a way, Juventus was a "known quantity", tough to beat, but easier to prepare for and both Dortmund and Real played the game they set out to play if you ask me.
Dortmund won somewhat comfortably with an inspired Andreas Moller. I remember thinking much went down to Paulo Sousa being a key player on the opposite side. Off the top of my head I can't think of another case of a CL winner being transfered out and beating his former team in the next final. Juve fans must have been gutted.
The 1998 final seemed to be played at a greater speed and intensity than I was used to. I was in awe of the phenomenal battle between Zidane-Davids-Deschamps and Seedorf-Redondo-Karembeu. Having witnessed such warfare, how could I not be bored to tears by ball-hogging tiki taka?
As in 1997, Juve got sucker punched, but I've no doubt both times that was exactly what the winners' plan and chances of success were pinned on.
With 90s Milan I think most, myself included, know there was the tasty Dutch Sacchi team and the resilient Italian Capello team, but we all somehow blur the lines and imagine one that was both simultaneously.