The Jesus wrote...
Honestly after the events of the past few episodes it seems to me that she'll wind up with Lelouch. I know, a couple episodes ago I was saying it would either be Shirley or no one, but I didn't anticipate her death and that did kind of sway my opinion. I agree that Shirley being dead might be what influences Milly to be more assertive about her feeling for Lelouch. Its also worth noting that she is the only one, aside from Suzaku, and eventually Kallen, who knew Lelouch was a former Britannian prince.
On the subject of her crying in the shower, it was at least in part about what Nina said. Nina basically called her on the fact that she was fake about everything she was. At Ashford she was the one who gave orders, but really didn't actually do much herself. You notice that it wasn't until after the incident with Nina that she chose to graduate, giving up her position of power as student council president, broke off her engagement to Lloyd, and started to do things for herself without hiding behind her name and status in society.
Milly had control of an army, not in the military sense, as the student council president. She was able to give out commands from behind the microphone and although she did play a seemingly active role in the events at Ashford, it was really the students who did all the work which is similar to Lelouch/Zero's role as leader of the Black Knights.
I really don't see Lelouch ending up with C.C. or Kallen. That's not to say that either of them being with him couldn't work. Its just that I don't see the writers taking either of those roads as it would seem too predictable, which would be uncharacteristic of Code Geass.
i think Shirley's death was planned from the very beginning, in the ending animation Shirley is portryed as an angel
EDIT:
um yeah forgot that that was after she died still sad about Shirley though :cry: