One of the things I have endlessly mused about but never done anything about was making Zile into a replacement for both shell and editor. The problem here, if you're not going to spend several years reinventing the world only to have people ignore you, is to find incremental changes you can offer independently of each other.
I have tried a few times in the past to give up using terminals and just use Emacs. In the past it's been too inconvenient because either you use eshell and interactive programs don't work (it looks like this may be largely fixed in 24.4) or you use term-mode and the usual keystrokes stop working, so you may as well give up and use a separate terminal window. (I guess that some degree of hand–brain rewiring is inevitable, as clearly e.g. C-c simply can't work consistently.)
Just now, I was thinking about a similar thing, namely my tendency to go back and forth between using Emacs commands such as diff and grep, and their shell equivalents. Why don't I stick to the Emacs versions, I wondered, since they tend to be richer (in the sense that their output tends to be marked up and you can interact with it in a specialised buffer)?
I think I've got it: it's because there's no history in Emacs of past commands WITH THEIR OUTPUT: yes, you can get a command history, and yes, the output from each command individually is sitting arround somewhere in a buffer like *diff-mode* or *grep* or *compile*, but there's no way to scroll back through your session (the closest thing is *Messages*).