(sorry if this question has been answered before, i'm new to this site)
What I should have written about was macro hacking and embedded languages and so on. That was what I really studied in grad school. But it didn't seem theoretical enough to be a thesis topic.
I doubt you were the first person to write a thesis which was unrelated to what you spent most of your time studying, and I know you weren't the last. I spent two years researching parallel computing, and then ended up throwing a thesis together out of two months of work on string matching and delta compression.