It's the same reason we say "a group of low-lifes" instead of "a group of low-lives" or "a pack of saber-tooths" instead of "a pack of saber-teeth."
When you take a single word and turn it into a compound, it changes it's meaning, and many times that causes the brain to process it differently. So, although 'friendly' changes to friendlier, user-friendly is a different word with a different meaning, so we use the simplest, most regular way of modifying it, and we get "more + user-friendly."
A simpler explanation might be that, as a general rule, we usually use the more + adj instead of adj. + -er for more complicated adjectives, such as those that are 3 syllables or more. Thus fast can turn to faster, friendly to friendlier, but 'copacetic' and 'understandable' will use the "more" + adj. construction.
