The Argentina forward, 28, is serving a three-match ban for his violent conduct in City's 3-1 win against West Ham.
Aguero has scored three goals in three Premier League matches this season, but Mourinho says his absence makes Pep Guardiola's side "unpredictable".
"He doesn't play and they have amazing options," said Mourinho.
"It is more difficult. When Sergio Aguero is available he plays, we know their formation."
Mourinho suggested any one of Kelechi Iheanacho, Raheem Sterling or David Silva could start as a "false nine" in the derby at Old Trafford.
"We have to reduce the unpredictability," added the Portuguese.
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The Spaniard, whose opening round in Munich contained six birdies, trails leader Wade Ormsby of Australia by two shots and Belgian Thomas Detry by one.
England's Tommy Fleetwood, who finished fourth at the US Open on Sunday, is tied for sixth, three strokes adrift.
Defending champion Henrik Stenson of Sweden also carded a five-under-par 67.
Fleetwood's compatriots Richard Bland, James Morrison and Matthew Southgate matched Fleetwood and Stenson's score.
"I felt like I played quite well, but not spectacular," said Garcia, whose Masters triumph at Augusta in April was his first major title.
"There's still three more rounds to go, so we're going to keep playing hard and hopefully we'll be up there on Sunday."
Manchester United manager Jose Mourinho says it will be "more difficult" facing a Manchester City side that does not include Sergio Aguero on Saturday.
[NEXT_CONCEPT]
Sergio Garcia shot a six-under-par 66 to share third place at the BMW International, his first event in Europe since winning the Masters.