One thing that's probably a good idea is to check ahead for things like areas with lots of doors. If you always have less than 26, then alphabetical is a good idea (as is numerically). If you always have less than 99, then two-digit numbers would be good, starting with 01.
Earlier, I was in the habit of renaming number-based stage map submissions to have a a leading zero so that all the stages would have the same number of digits. It helps when listing files alphabetically. But with Super Mario Bros. 3, whereby there is one stage that reaches 10, namely "6-10", it looks weird to have "World 1-01", etc., all because of that one case. From around that point onwards, I didn't always add on leading zeroes, because some file browsers (like my grossly outdated CompuPic Pro that I still use) has the ability to sort files alphabetically as well as numerically, meaning that 6-10 appears after 6-9 as it should, instead of before 6-2.
I guess that was kind of tangential to the discussion. But planning ahead is a good idea, because it's not so fun to have to go back to previous maps to change things for consistency's sake because of something you discover later.