Do you agree about the relative inefficiency of theoretical discovery?

In presence, yes. In degree, no. Even the efficient market hypothesis presumes (indeed, requires) some delay inefficiencies, and even restricting to fields where economic incentives are very, very high we see some pretty significant delay inefficiencies.

The modern containerization revolution is dependent on certain types of math and metallurgy being available, but the underlying tools were probably available before the first world war (and, indeed, would have been even more useful if developed it then, due to varying railway gauges), but didn't take off until the 1950s, and were controversial for a near decade after that. Supply chain management innovations since, including as recently as WalMart's (and to a lesser extent, Amazon's) shipping models, have trailed their underlying technologies what I'd estimate to at least a decade. Even purely digital financial markets have remarkable innovations that seem obvious in retrospect yet weren't around for the longest time.

Philosophy seems to have further delays on top of that, but that they're present in other fields suggests that we can overestimate the impact of some individual causes.

What are some other signs of likely low-hanging fruit for theoretical progress? What’s up with decision theory having so much low-hanging fruit?

I've been looking at things from a more basic model. Innovation seems to be the ability to non-randomly(1) put together component concepts(2) into an implementable (3) result, some of the meaningful attributes will be where :

• Where the typical connections of thoughts are non-complete, where they are based on untested or (especially) false assumptions.
• Where we have unusual component concepts available, or (more commonly) where the average researcher is discouraged from outside component concepts. Interdisciplinary discoveries are major soft spots, here.
• Where the costs of testing hypothesis are very small, have recently become smaller, or are unusually small for our skillset but not the average researcher.

These seems to cover decision theory, although it should be noted not all of the side effects of these attributes are beneficial.