The height

The pint sized A+/A list actor is using much smaller lifts than he has done in the past.

Maybe he is finally comfortable with his height.

Tom Cruise

First off, this isn’t just done for Tom Cruise obviously. A majority of leading men in the history of cinema have come across fellow cast mates that are taller than them. A majority of films in the history of cinema have had to create ways to even cast mates’ heights out for proper framing, desired characterization, etc.

Robert Downey Jr. – 5’9″

Ben Stiller – 5’7″

Al Pacino – 5’6″

Humphrey Bogart – 5’8″

Dustin Hoffman – 5’6″

Plenty more where that came from too.

There are a number of ways to make one actor appear taller than they really are.

Shoes/Boots
Apple boxes
Forced perspective shooting
High and low angles
Posture variances
Trenches
Risers

The best practice is likely casting, but there’s not always the freedom one would like in that respect. It’d be very difficult to always simply cast a shorter actress to act alongside a short actor.

So there’s no big secret here with Tom Cruise. His actual height? Who knows? It’s been reported to be 5’7″ – 5’9″. Likely somewhere in the middle. – Source