This is something I’m very very interested in solving, as the UX around cross-instance interactions is so painful. We’d be more than willing to experiment with any ideas in WriteFreely to help move this along.
URL protocol handlers sound like a potential option, but I can imagine that they’ll fall short for people who have multiple accounts, including across various fedi platforms, since only one instance could be registered to handle the protocol. (I believe that’s the case? Correct me if I’m wrong.)
But maybe we could combine this with something else I was thinking: a browser extension. My idea was to create one that would let you authenticate with all of your fediverse accounts, so when you want to perform a remote action, it would simply let you choose from your list of accounts to interact from. This way, you could also perform certain lightweight actions within the extension itself, and skip loading up your entire instance – such as for follows, likes, or boosts.
Maybe then the browser extension would register as the handler for this custom protocol?