The difference between Heynckes squad in the treble year and Pep's a year later was that Heynckes had a set A team and somehow a set B team, too. The B-team then with Starke, van Buyten, Rafinha, Contento, Gustavo, Tymoschchuk, Pizarro, Gomez and Shaqiri - added with first teamers that often just played a half and Emre Can or Höjbjerg - before Kroos was injured even Robben was captain of that B-team and Heynckes even had the teams in the region for friendlies. The 9:2 win against Hamburg or a 6 to something win away in Hannover were made with this B-teams. Schweinsteiger and Lahm did not play a single Bundesliga match from the day we had the Bundesliga title until the CL final was wrapped.
When Pep came Gustavo, Tymoschchuk and Gomez went. Emre Can went to Leverkusen with a buyback-clause. The A-team got bigger when Lahm went into midfield as Rafinha was a fixed starter. Götze and Thiago came and were part of a big rotation of the A-team, too. And some guys who were "clearly" no part of the usual starters like Shaqiri and Contento were injured. The mixture Guardiola then fielded in the weekend matches after the titles was done were players that were hoping to play on Wednesday or that thought that with playing Saturday they already weren't an option for Wednesday - or youngsters that did not have any practice at all. That just did not really work out.