Byzantium was the continuation of the Roman Empire, but in my humble opinion is a quite distinct culture in its later form. Byzantium as the Empire without Rome, which is no longer in the integration and assihimilation of foreign religions but in the forced conversion to the monotheism, the polarity of the empire located further east, the dominant multiculturalities of the empire have changed (the Greeks, the Rus, Anglo-Saxons, Armenians, Georgians, Serbs etc ...).
I mean, the claims and the heritages of the Roman Empire through Byzantium are "legit", but the various cultures which dominate these two "entities" are really different (in proportion and some other encounters are totally new to the empire and will participate in forging its new identity).
For me it's like trying to do a Civilization of modern Turkey with an Ottomans leader, or an Ottoman Civ with Ataturk as leader. Yes the historical continuity is obvious, but in term of "archetype", in term of cultural constitutions of the land, in term of identity, they are distinct enough to be highlighted in an historical context game and make an interesting Civ to play.
And IMO, China, India and Arabia derserves the same treatement. Well China is a bit complicated for marketing reasons. But I wouldn't mind having Gandhi / India and Babur / Mughal in the same Civ game for exemple. Or having Charlemagne with Franks, and some leader of industrial France, instead of two iterations of medieval-renaissance-ish France. Well, Arabia is a mess since a long time, what it ever means for Saladin or Harun al-Rashid leads Arabia ?
They made good effort with Gauls instead of Celts, in the sense than Gaul is a blobbish roman term, BUT allow to focus a bit more on a more distinct design of leader, units, bonus, etc .
Anyway, with the current system of alternate leader in Civ 6, they can't show how distinct enough are these phases in the History of Civilizations. Alternate leader right now don't encompass enough distinctions to make interesting design for Byzantium IMO. They were the most influential civilization in medieval europe, the most coveted city of Constantinople, the crossroads which make Byzantium a marching powerhouse, which preserved immense knowledge (which will be largely lost with the 4th crusade), which had a form of religious fanaticism , and a singular aesthetic around Christian theology (the HRE crown is inspired of a Byzantine crown, all their clothings and jewelry were so singular).
And all their singular units (the "Immortals" kataphractos armed with maces, the Varangian guards, the Dromons, the liquid fire grenades which will be adopted by the Abbassids and Fatimids, the most powerful navy of medieval Europe until they were ruined by Sicilio-Normans, the Armenian border guards, etc ...). And by the way their impressive architecture.
Basil II leading Rome would just feel a bit odd for me, he is the perfect example with its dynasty of the cultures that forged the polarized empire further east and the cultural "clashes" with slavic cultures. And we will lost a lot of gamey thing if we mix Byzantium and Rome in next the game, again just my opinion. But I must admit than some other leaders of the early part of "Byzantine" period could totally work as alternate leader.
For Macedon, it's a bit tricky, I don't mind Alexander leading Greece, but I must admit than he was way more than Greece. So having its own thing with Macedon is okay-ish in Civ 6. It's just than for me it is a problem rather from the beginning, a lot of slots in the game have been devoted to a "similar" period for Hellenic civilizations. I would easily cut Sparta at launch to have something as influential as Byzantium (well I'm a bit biased because I am way more interessed in the influence of late and medieval roman empire and their relations with islamic empires and crusaders, but for me all their archievement deserve to be represented if you want something from medieval europe at launch for an historical game). As always, it's more a question of game design, "Greece" naming was not even a thing it is period. Alexander should lead Greece Civ, if he had a bonus related to hellenism spreading. But I would not mind having Civ 7 with Phillip II leading Greece only through a bonus related to League of Corinth, or some other gamey design, instead of the currents ones, which take a lot of slots, and are not that good.
At the end, I wouldn't mind having Civ 7, with Rome leaded by Justinian or Constantine at launch, to not have this never ending debate
But I'm happy to have Basil II which highlight something more specific and which for me, don't work at all as alternate leader for the current Rome in Civ 6. (and Byzantium gift us of an amazing ost too )
Edit : On a technical level, the work on the leaders already seems very costly in resources for the team, without being very interesting on the gameplay aspect (even if it is an interesting aspect for the side "to represent another period of a "same civilization" or "to represent a civilization which was a bunch of city states or tribes, as renaissance italy, ancient greece, or celts), at least not interesting in civ 6 maybe it will be in 7, but personally, I do not see a problem that they abandon the concept, to have more distinct civ in return.