Incremental search isn't too bad once I found out about bind and the other key bindings, as the arrow keys are some distance from the home keys.
Lack of Alt+. quickly became annoying. It's so useful; meanwhile, prefix search isn't a significant improvement over incremental search, and I usually know ahead of time whether my command is in the history or not, so being prompted an irrelevance is more annoying than having to type Ctrl+R in readline. I disable auto-completion in browsers, Google etc. for similar reasons.
You're right about not much else. Command substitution is the only thing implemented, not subshells or process substitution. I probably exercise my shell more than average, so I don't think fish is feature-rich enough yet for me.
It's a good thing the design goals have been updated to remove "a large performance decrease [...] is acceptable in order to improve [modularity]". That would have been a total killer. Process forking is often a performance limitation for me in the shell, so I strive, wherever possible, to use the builtins that fish so proudly spurned.
I believe Alt+. (or any kind of history substitution) hasn't been implemented by design. I don't have references handy but they should be easy to find.
Incremental history search is just type something and then up arrow.
The rest of your questions I don't know the answers but it wouldn't surprise me if there were none. Fish prefers to have a simple and coherent syntax to a concise one (though I agree the text substitution is annoying – it seems they usually put the subshell result in a variable and expand that in the string).
This helps understanding their design goals http://ridiculousfish.com/shell/user_doc/html/design.html