Pretty much the answer to most of these is either lazy writing or plot device. Plus, if you recall, Itachi was able to use BOTH Amatersu and Tsukuyomi, despite his Sharingan in it's regular state. However in Shippuden, he always uses it while his Mangekyo ie active. Simple reason is the Mangekyo was yet to be introduced.

Same with Sage Mode. It was yet to be introduced at the start of the series, so that's why Hashirama didn't use it.