Personally I believe that Charles' Geass on Nunnally wore off when he "disappeared". Its just that she didnt realize that she could open her eyes and see since...she probably never even tried opening her eyes since the day that she was put under the Geass' effect. But man, was that a shocking moment...I mean, its something that we all knew was probably gonna happen eventually but I didnt expect it to happen like "that".
As for "will Lelouch use his geass on her?", I'd like to go with "No". I'd like to think that his love for his sister beats all and that his respect for her will refrain him from using his geass. C'mon, the guy promised her that he'd never lie to her. (in reality he really never did, its just that he eluded the truth...I dont think that they're the same thing) But than again Lelouch has really come a long way since the day he has obtained his geass and he is now actually truly respecting the lives of the people that died for him while he was ZERO, like Rolo (him showing respect for Rolo really surprised me and showed me he truly has matured) and Shirley. At this point we'll never know, the last few episodes have been throwing major curve balls at us one after another.
As for Kallen vs. Suzaku: We'll probably find out in the final episode. (We'd better....) Personally I'm rooting for Kallen. Suzaku has NEVER been a character that I liked.
Seriously, anything could happen in the last episode...hell, Euphemia could come back for all we know. (O_O)