Alexander is here to stay and always will be.
Now, don't get me wrong: Alexander's My Man, I did my thesis on him and his army, I was quite despondent when I turned 34 and had to recognize that by the time Alexander was my age he had already conquered the known world and died. As an individual Over Achiever, he's in a class by himself.
But.
As a Civ and Leader, he's pretty darned limited. He has a World Class Army (for the Era) and he conquers people. Big Whoop. So dd most of the other rulers in or potentially in the game.
The way to include Alexander, and show his real historical influence, would be that after he conquers his first Capital, he disappears (died young) and is replaced by a Leader of your choice: Seleucus Nikator of the Seleucid Empire, Ptolemy Soter of the Ptolemaic Dynasty of Egypt, Mithradates of Pontus, or Lysimachus of Macedon.
Each an entire new Civ and Leader Traits, but related to the Hellenistic features that represent Alexander's Cultural and political influence (and military, to be sure) on the Middle East.
As to Byzanitum as an Alternate Rome, let's not go there. For one thing, read Wickham's
Inheritance of Rome, and you'll find that just about everybody from Constantinople to Spain used Roman terminology and forms in administration, military, taxation, and tried to mimic Roman systems of governance, and that included peoples as different as the Franks, Vandals, Lombards, Goths, Byzantines, and later Merovingians. You could end up with a half-dozen 'Roman' Alternate Leaders, none of which were ever Roman!