Since you don't know which one, the letter or the CV, will be read first, you should optimize both.
I wrote an article a few weeks ago on the same topic which is relevant (http://lifehacker.com/tips-from-a-recruiter-dont-make-me-rea...)
Why do some companies not accept cover letters? For one, nobody wants to read them. Keep in mind, nobody wants to read cover letters OR resumes. They want to have a conversation, and they want to be able to determine as quickly and accurately as possible whether or not that conversation is worth having. This can be quite prone to bias.
Most cover letters simply reiterate what the resume says, but in a condensed format, along with some fluff about how hard they work and how strong their soft skills are. It's usually fairly pointless, and some companies ask for them as a bit of a test of your interest. Companies that don't ask for them likely don't feel they are useful, and would rather have their recruiters looking at resumes (and hopefully actually having conversations) than reading traditional formatted letters.