The fact that the Enigma never encoded a letter as itself was a significant flaw in the design, which could presumably have been avoided.

Better training for the operators would also have helped, e.g. don't start every message with "Heil Hitler". Some of the services were much better than the others IIRC.

The Kriegsmarine had more secure procedures for transmitting the setting key, added more rotors for more possible combinations, and eventually introduced a new Engima with four rotors instead of three. Their transmissions were more difficult to decrypt.

The Luftwaffe were far more lax in their procedures, and Hermann Goring sent many trivial messages that made it easy for Bletchley Park to decrypt.[1] From early 1940 to the end of the war, air force messages were routinely read.

[1] From https://en.wikipedia.org/wiki/Cryptanalysis_of_the_Enigma: "Luftwaffe chief Hermann Göring was known to use it for trivial communications, including informing squadron commanders to make sure the pilots he was going to decorate had been properly deloused."