While it's true he could have used the sonar more, it's not really a flaw of the movie. Burton didn't reuse Batman gadgets as well. Hell, it's now a well established TV trope, of practically every movie series ever made, that certain deus ex machina devices, that could be used multiple times to save the day, are completely forgotten in future instalments.
To call it a specific flaw of Nolan Batmans, is exactly the kind of scrutiny that some seem to apply to his bat films exclusively, and fail to see, that the same stuff can be found in practically every hollywood action film.
I also completely don't understand how can anyone say, the trilogy lacks gadgets. Throughout the three films, Wayne uses batarangs, mnemonic-capes, magnetic grapple gun, sonar vision, smoke bombs, throwing bombs, sonic boot heel, tranquilizer batarangs, emp gun, wrangler, periscope with night vision, sticky bomb gun, crime scene investigation equipment and more. Thats an impressive list for any superhero, and more stuff than the gear of previous Batmans (even if we discount TDKR).
Truly, sometimes it seems like some people would only be happy if Nolan included all the elements from the 60+ years of Batman mythos, inside his 3 movies.