The best squad I've ever seen in my life was Milan 1989 team. Their defence was stellar with Baresi, Maldini, Costacurta and Tassotti. They had the likes of Donadoni, Ancelotti, Rijkaard and Gullit in midfield and Van Basten upfront. Yet that side won just 2 CL in a row, they came third in the Serie A of the 88-89 and second place in the year after. Why would such a side struggle so much? That's because the Serie A was fiercely competitive with smaller sides being able to afford top top players. The margins of error were so small that teams with exceptional players would end up fighting for relegation or even get relegated. For example Inter ended 13th during the 93-94 season despite having players like Bergkamp, Zenga, Toto Schillaci and Bergomi in the squad. Fiorentina got relegated during the 92-93 season despite having players like Laudrup, Batistuta and Effenberg. I don't think that the EPL is as competitive as the Serie A at the time. However its the closest thing I've ever seen to it.
Having a less competitive league means that one have a lot of leeway in terms of resting players for the CL. It also means that one can get the foot off the pedal for 2-3 years (the so called transition period) as the club would still be able to win a trophy or two keeping fans happy. Not to forget that if things get really bad then Bayern can easily bankroll a rebuild, probably by poaching their rival's best players. I mean we're talking of hugely one sided league were Bayern had been winning the league since 2012. There's less pressure and more room of making mistakes there then let's say in the EPL were one slip too much might push United from a comfortable 2nd place to 6th.
We really can't compare ourselves to Bayern. They are in a different world to ours.