Leander didn't have major changes, but his original facial characteristics resembled that of Echekrates.
Cleisthenes was drawn with red hair, instead of grey.
The tyrant Hippias seemed to have a bigger role in the story, but ended up appearing a handful of times in the first chapter, disappearing completely for Chapter 2 and onwards and only mentioned once.
Athena also had red hair, but ended up appearing all gold.
Word of God: The Commentary Section at the end of the book provides some of the authors' thoughts and ideas:
The unnamed general that accompanies King Kleomenes to Athens is his step-brother, Leonidas (yes, that same Leonidas who fought at Thermopylae).
Sparta's presence in the story was to be a Foil to Athens'. Sparta was run from fear and it was incredibly militaristic and oligarchic, while Athens is far more democratic (not to the same extend as today, though) and had to find the courage to rise from the obstacles.
Similarly, Hero and Leander's myth represents the fear of the two lovers. Just like the Athenians had to believe in Cleisthenes' vision, Hero and Leander had to believe in their love, in order not to end up like the two persons of the myth.