As observed earlier in this thread, many of the leaders were villainous in some respect, and for all of her unpopularity there has been a lot of retrospective scrutiny of where that reputation came from and how much of it was unsubstantiated smearing. Also, Kristina.
I don't think Kristina can reach the unpopularity that Cixi received in China. Kristina did abdicate the throne and caused a "betrayal" image. Still, she also had the image of a book-lover, fond of new knowledge and high culture, which became her civ ability - there is a significant positive side of her. On the other hand, Cixi is basically being remembered as a ruler who misappropriated the funds of the navy, put an end to the modernization reform, executed the reformers, try to declare war on all the nations in the world, and received a humiliating defeat as a result. In general, she is usually considered as who kicked Qing/China out of the path of modernization, that's a very different image compared to Kristina ("Minerva of the North"), CdM (patronage of arts), or Seondeok (patronage of religion and astrology).
I am not necessarily saying she is "bad" at ruling a country and shouldn't be considered. Cixi's strategy of ruling is actually very adequate for a ruler who bears Inner Asian traditions, who would prefer land power over naval power (therefore ignore the navy) and insecure about conquered people's rise in power (all the reformers are Han Chinese, and they did try to overthrown her, so Cixi fought back). Viewing all foreign counties as uncivilized barbarians is also a tradition of Chinese rulers (we did see ourselves as the center of the world before beaten up by the British, you know). However, Cixi already lived in the modern era; all these traditional strategies, no matter how effective they were in the past thousand years, became obsolete in the 19th century. She continued these strategies, together with her unwillingness of reform, and failed miserably.
And as a result, Cixi's anti-reform, anti-modernization position could lead to a design problem: currently, many of the modern leaders we have are reformers - especially Teddy, Pedro, Menelik, less so but still Curtain, Laurier. Menelik, the only non-western modern leader currently in the game (let's just left Gandhi out of this discussion), has his ability themed around modernization (Council of Ministers). How would an anti-modernization non-western modern leader fit into a progressive narrative is a serious question. Anti-colonialism is also out of the question as Cixi didn't mind colonizing Xinjiang under her rule as part of the "preferring land power" strategy (Qing is still an Empire at that time).
I'm Chinese, so I'm certainly biased here; and as far as I can tell, Cixi wouldn't have a great appeal to the Chinese market/community. Moreover, she would hardly fit into the current theme of the leaders. So I still think Cixi as an alt leader is very less likely.
I think her chances of being considered are quite likely given that the high point dynasties in Chinese history are the Qin, Tang, Yuan, and Qing, and of those the Yuan and Qing differentiate more from the Qin both temporally and culturally. Rest assured that if the devs wanted a Mauryan leader for India and an Occitan leader for England, and now have a Mongolian leader for China, they were definitely looking at Manchurian options as well and were considering prioritizing that over a return of Wu Zetian. Also, again, Kristina.
That's a massive wall of texts trying to comment on Cixi, so let's talk about something more relaxed: In terms of the conquest dynasties you have mentioned, there is a 3rd "foreign" dynasty of China - Tang. Tang rulers are not ethnically "Chinese", and have introduced many political and cultural traditions that were very different from those of the previous dynasties, such as the heavy use of the foreign legion (An Lushan belongs to here). Early Tang emperors also have the title of Tengri Khan ("Khan of Heaven" in Turkic languages) when they incorporated many Turkic tribes/Sogdian city-states under their rule.
The problem of taking this as a game design is that, the Tang rulers were from obscure ethnic origins (probably Xianbei, but Xianbei is already an inhomogeneous group), and we cannot invent a nomadic civ out of thin air.
In the end, I think the best alt leader to fit the theme of conquest dynasties is still Kublai Khan. As for Qing, technically, every Qing ruler after Hong Taiji is the co-ruler of Mongolia, so that's a wide range of choices.
Edit: Typo. Too much words.