Tomorrow's Dawn:
Responses to your points:
1) Disagree - to use your example, the changes in Rome across these civil wars are nothing like the differences that China experienced across these thousands of years. But we aren't even talking about the very real differences between Han and, say, Tang - we are talking about the much more dramatic differences between the Manchu Qing and the Ming.
Further, I never proposed every Chinese dynasty should have their own civ. Agreed that that would be unworkable, especially in the ancient era. Probably a bit more division and struggle is needed (barbarian spawns? collapse into independants?), but that is a more difficult question, especially given the vast number of years per turn in the ancient era.
But by the 1600s there is a reasonable relation of years to turns, and a HUGE upheaval (the chaos of the end of the Ming and the conquest of the Qing) that just can't be glossed over as a turn of anarchy in changing civics, and really needs a fullout invasion to represent.
The same is even more true by the early 1900s, where the year to turn ratio becomes even better - do we really propose to gloss over decades of civil war and anarchy as some civil change or, to use your suggestion, roleplaying?
Besides, there is an implicit assumption underlying your argument - that the conquest of the Ming dynasty by a northern 'barbarian' people, the Manchus, was somehow equivalent to a change of regime within the roman civil wars. In fact, to quote your opening line, it would be exactly "the way civilizations are structured" within the mod to model the Manchu Qing dynasty as a seperate force - because that is the way the Mongol Yuan dynasty is treated.
2) I agree with Ben - Manchus would work fine as a Jurchen respawn. Might currently be planned as minor, but that plan could be changed. However, maybe there are reasons why a full Jurchen civ would be too shortlived with the Mongols on their heels, and in that case leaving them minor and incorperating the Manchus wouldn't be too problematic (for example, india first appears as a minor and then has a full civ spawn).
3) Your account is very much in line with standard historical accounts in China - but remember, these serve a political purpose. Qing and the Manchus MUST be described as Chinese, because the current political line is that China's current borders and ethnic makeup stretch back into history as some kind of essential truth, when in reality things are much more complex. Please remember that the standard politically correct historical interpretation in China is that Genghis Khan was a Chinese general who unifed the country.

Yes, the Manchus adopted many Chinese institutions, but they preserved just as many aspects of their own culture and governance. No, I cited Elliott as representative - I don't think there is any implication that mentioning one person means one's argument is limited exclusively to the work of a single author. Yes, there are all kinds of historical debates going on, but the idea that the Qing instantly became just as 'Chinese' as the Ming or Song is somewhat a relic of a politically motivated conception of history. Please remember that Qing history is still a VERY politically sensitive topic, and scholars are not free to write whatever they wish. Even tv shows have their scripts heavily censored to eliminate any suggestion that these conquest dynasties were not fully Chinese, as well as to eliminate any pejorative terms describing northern nomadic peoples.
As for your other points on the republican revolution - I think you are overestimating the importance of the facts you state. Yes, some manchu people cooperated with the rebels, this would be seen in any revolution. But no, your argument about this being an attack on the 'ruling class' is drifting way too close to the politically correct marxist class conflict interpretations. Sure, that element was present - but the ethnic dimensions of this revolution cannot be underestimated. To go to just one story - Mao Zedong shaved his hair, and forced his friends to do the same (upon their conquest the Manchus required all Chinese to adopt their traditional manchu hairstyle, and many revolutionaries used shaving this 'foreign' hairstyle as the symbol of their resistance). But more prominently, any reading of the writings of this time shows that this was an anti-Manchu revolution, blaming the Manchus for Chinese stragnation, and desiring homerule - the language is quite clear on this point. You can't just reimagine this as a codeword for 'ruling class'.
4) Yah, it may be too difficult to plan to have europeans own colonies given the map. More I meant wars and unreasonable demands (gold, resources?) could add to the pressures on the Qing. But you are probably right that this is too hard to model, so the Qing civilization should be structured so as to go unstable mostly on its own (or with the help of japanese invasions)
5) I think the rise of the Qing and then a Chinese respawn only improves how intertesting and diverse the pre modern and modern periods become. But I respect we have a difference of opinion here. As far as the game mechanics, I think they will work quite well in this case - essentially another Mongol invasion, but with a greater chance of lasting longer before it faces a strong potential challange from a respawning China. I think this is very fun, and would make the 1600-modern era in east asia a great deal more dynamic. Particularly, I think this will make the early 1900s alot better, and we will see alot of interesting possibilities for East Asia.
Anyway, I think I will avoid drawing this thread even more into a historical debate, and make this my last reply in our debate. I think we have stated both sides of the issue pretty well.