In almost every case, proportional fonts are superior. They look better and they’re easier to read. One obvious exception is when programming but, even there, not everyone agrees. Still, most programmers are pretty firm in their preference for monospaced fonts when programming.
Some writers also like monospaced fonts when preparing their manuscripts, probably for atavistic reasons involving typewriters. I thought that was silly when I read it but then I realized I do all my writing in a monospaced font even though Emacs would allow me to easily use a proportional font if I wished.
All of that notwithstanding, it remains true that monospaced fonts are a bit harder to read. Blake Watson has a very interesting post on almost monospaced fonts, something that I’d never heard of before. The idea is that the characters are mostly the same size except for a (very) few letters requiring more space, like M and W, and some requiring less space like i and l. Watson’s post gives examples of the same text written in a (strictly) monospaced font and in two versions of an almost monospaced font. The almost monospaced fonts do look better and are a bit easier to read.
I haven’t tried but it probably wouldn’t be too hard to arrange for Emacs to use one of the almost monospaced fonts for certain file types or directories. Watson claims that even using them for programming isn’t bad so you could always use it as the default Emacs font if you wanted.
Don’t judge the issue without taking a look at Watson’s post. It’s interesting and revealing and you might even find that it points to another way.