My grasp of Japanese is virtually non-existent, but I noticed this as well. Taking an example from the post, I find something like しっけ easier to parse than the romaji shikke. The latter form just feels clumsy for reasons I can't really articulate.
It also makes the pronunciation a little easier at times. If I read "desu", I read it with a fairly pronounced "u" sound. Reading です, on the other hand, I know without really thinking about it that the う sound is typically very short.
Really though, you can learn hiragana in a single sitting using mnemonic trickery and you can commit it to memory using a spaced repetition or flashcard system in a few days. Not learning hiragana and katakana seems much more of a hindrance than "wasting time" by learning it.
Learning 2500 kanji from the beginning is a major cognitive task that shouldn't be a primary focus, nor is it in native Japanese language pedagogy. But learning the kana is simple, again I learned them as an adult and had them down cold in a few weeks of active classwork. My kanji retention is terrible, but learning materials almost always give the reading of kanji using furigana, and there are useful tools for annotating web pages, etc. with furi readings.