I've encountered a rather frustrating UI issue as a recent Emacs convert and would love to help think of a way to fix it. Bug #11172 references this issue, but there was no comment or resolution.
The issue is that the echo area, which is used heavily from the message function, shares screen real estate with the minibuffer. This normally isn't a huge issue but if the user is actually using the minibuffer to enter text, the prompt and the text they have entered thus far is overwritten by some unrelated message and can only be wrestled back by typing more.
The example I encounter frequently is doing a TAGS file search and hitting TAB to complete. The tags system will fetch a completion and simultaneously log a message that its reading the TAGS file which will completely overwrite the completion.
A contrived example:
emacs -Q
M-: (run-with-timer 5 nil (lambda () (message "hello"))) RET
M-x
The prompt will be overwritten by the message "hello".
I don't know what the best solution is. Two ideas I've had are:
1. Suppress messages to the echo area if the minibuffer is waiting on input. The messages could display after the minibuffer stops waiting (or not at all and they'll just log to *Messages*).
2. Divide the minibuffer (horizontally?) into the minibuffer proper and the echo area. Maybe the division could only happen when there's something in the echo area. Something tells me this approach is much harder and more controversial.