Rome into Byzantium into Ottomans really brings home one of the issues of how civ switching doesn't really work very well. The fantasy that we have when we play a civ is that we take them from the stone age into modernity and we craft them through that time, maintaining them across history. The Eastern Roman Empire was conquered and destroyed by the Ottomans, they didn't 'become' the Ottomans. If that was a Civ game it would be one player wiping out the other one.
For what it's worth, I like the concept of a civ evolving over ages, going from Greece to say Spain, well it's kind of cool. It's just so crude at the moment. If instead I remained Greece, but had the option of taking on more and more elements of Spanish culture and personality as time goes on, well that would be good, and maybe at some point I can choose to rename my cities and my civ as Spanish, but it would less abrupt, and would be due to the consequences of my actions and choices.
Actually, I kinda like exactly the transition Rome-->Byzantium-->Ottomans, since the Ottomans took over and mirrored certain institutions and administrative practices from the Byzantines.
The example used by Ed Beach in the promotional run-up was similar: Londinium was a roman founding, Anglo-Saxon settlement in the early Middle Ages, then to be taken over by the Normans. Each transition by military force. Yet I grant your point, that especially "hostile takeovers" are odd, if they appear to happen in the "dark" between ages, outside the actual gameplay.