"He's one of Real's best signings, of course, but you can't forget the players of huge quality who joined Real this season," said Puel, whose side host Real in the first leg of their last 16 tie on Tuesday.
"We know that he's a coach who is capable of making his team work. But it seems that there's much more balance this season, with more dutiful players, who are there to maintain that balance and allow the 'stars' to express themselves."
Real were knocked out by Lyon at the same stage of last season's Champions League and have not defeated the seven-time French champions in six meetings in the competition.
Chilean coach Manuel Pellegrini was at the helm last season but was replaced by Mourinho last summer, after the former Chelsea coach had led Inter Milan to a first Champions League title in 45 years.
Real, nine-time European champions, have been eliminated at the last 16 stage of Europe's premier club tournament for the past six seasons in succession.