While she'd be awesome for the "powerful doctor" parts, I'm not sure she's "Zany" enough for the role. The Doctor is IMO borderline insane a lot of the time, and thus, not sure she can pull that off. Hence why IMO The Master is such a great Nemesis to him, because of how
similar they are, rather than different. The Doctor is very
very close to The Master, kind of like a Dark Reflection, and so anybody who played The Doctor without the funny/zany would be a departure from the (last few at the least) depictions of him. There's a reason why Clara was able to FAKE being The Doctor in an episode, because she (the character and the actress)
does have that zanyness to her.
Not saying Atwell
can't be all that, and I think she's a great actress, I've just never seen it to date. And she's on the young side. Not that they haven't done it with Matt Smith, but keeping an older Doctor for a while could be a good thing.
As for who could pull it off? I'm not sure, but the
range shown by
Olivia Williams (played Adelle DeWitt, the head of the Dollhouse in that show) could pull it off. She has the "air of power" about her for it. I'm not sure of the Zany, but enough range was shown in that show that I wouldn't put it past her. Other female options I'm sure are also legion. In the "it would never happen but would be awesome" category would IMO be Whoopi Goldberg. Think Guinan in ass-kicking mode. How is that image not awesome?