Doctorate Brown, MIT, Cornell, etc: chances for nontraditional student?

Yes, I'd say the issue with low grades could be a stumbling block. Sure, you can make excuses, but the truth is grades are considered, as are writing samples, GRE results, reference letters etc. Schools simply don't have to admit students who aren't consistent top achievers. Saying that, if you get the chance to meet the people making the decisions and get in there and make a positive impression and have references that are very strong you might have a chance. I wouldn't limit myself to Ivey schools either. The school's name brand doesn't matter as much as the actual work you produce as a grad student and the professor you work with.