Well that's about the worst game I can recall from Allegri in the CL for Juve or Milan.
Juve were extraordinarily passive and the whole game up until Bayern's second goal was just waiting to see how many goals Bayern would score.
Juve's defence was stretched too wide. That meant the defence was very deep and that meant the midfield had to go very deep in order to limit the danger of Bayern playing through the middle and Juve's forwards then got pulled back.
But that ended up being self-perpetuating: Juve couldn't get the ball, so the strikers came deep, so Juve couldn't keep the ball when they did get it.
There had to be a plan for Juve to keep the ball. The simplest thing would have been to leave Mandzukic high up and play long to him. That takes Bayern's press out of the game and it would be hard for Bayern's non- centre-halves playing centre-half to cope with Mandzukic. Not once did Juve play a targeted long ball to Mandzukic before Bayern went 2-0 up.
That lack of plan to play out made the first half scarily reminiscent of the last tie against Bayern. The only difference was that Juve at least weren't trying to give the ball to Pirlo all the time, so most of Juve's give-aways weren't in overly dangerous positions.
Bayern played a very good first half and that's one of the best plans I've seen from Guardiola. The wingers were really wide and by pushing the fullbacks into midfield he made Juve make a decision: be out-numbered badly in midfield or leave Lichtsteiner and Evra one-on-one against the wingers. Juve did have a response and ended up being outnumbered in midfield and unable to stop Bayern's wingers getting one-on-one with the fullbacks.
That said, Bayern didn't actually create that many chances through that period of the game and Juve still got themselves into a number of good positions.
Bayern lost intensity once they went 2-0 up and Juve, since they were out of the CL at that point, had nothing to lose and so they became more aggressive.
In the second game, Juve need to be more centrally focused. That will risk being opened up by a good switch of play, but I think that is a necessary risk. With the defence more compact, the midfield should be able to be a bit more aggressive and that should help the whole Juve team to play a bit further up the pitch than they did last night. It may even get a striker or two high enough up the pitch to give Juve and out-ball and a chance at keeping the ball and avoiding the game being nothing but incessant Bayern pressure.