Defensive transitions?
You can compare them to other players of similar performance on
tackling and
interception stats, they don't strike me particularly worse than any other midfield in the competition except Atletico, that play with 4 guys being paid to do that role.
Chance creation?
Kroos was the midfielder with most key passes, Modric being 9th.
No other team has a midfield combo with two players on the top 10.
Modric is 27th in interceptions, only 0.1 below Rakitic who basically plays most games for that, and above holding midfielder specialists like Fajr, Pizarro, Wass, Lobotka or Borges.
They're not creative in a tiki-taka way, but they've been the most complete midfield trio of the world for the past 3 years, if you add Marcelo to their mixup they become even better. Modric can recycle possesion and drive forward like no other in Europe except Hazard, KDB and Messi while having a workrate none of the past 3 display. Kroos is a distance maestro that can pass it short like the best in the game right now and a long ball that, as you said, opens any opportunity for Real Madrid, be it different wing, same wing or center.
Nevermind that all of them can bomb you from 35m range finding goal, how many teams have the luxury of fielding a 3 men midfield that covers every aspect of the game?. They only suffer when the ball goes above them.
Rio, Carrick, Vidic, Evra, Giggs or Scholes were 6 years younger too, the fact that United managed to get back into title winning form and reach a UCL final adding Bebé, Smalling, Valencia and Chicharito once Ronaldo left might tells us that it's not so black or white about a single player being the key difference between being good or bad.
First thing to address might be what kind of signal sends to the squad selling Ronaldo and bringing Mariano, everyone in that locker room might've thought from the start that the team wasn't asking from them a lot this season, and maybe that their time to leave will come in the next 1/2 years with the president not interested on spending the proper money to give this roster another go.