Just wondering whether, seeing as Martin Septim is described a s dragon born in Oblivion, and the blades say they await the rise of the next dragon born, the hero of Skyrim would therefore be an heir to the Cyrodiilic throne?

No. Or not necessarily. There's more than one line of Dragonborn. They were referring to the Septim line, which seems to be dead with Martin.

Think of the Septim line as the most well known noble, everyone knows him and knows he is famous. Its just that the Septim line was the longest and last bloodline, and when the blades were talking about the next dragonborn, they are referring to a Septim, as the rest of the separate dragonborns are assumed long gone...until now! dun dun dun!!