Interesting. Like most people I use the romaji input method, type 'k a' and 'か' comes out, but the kana input method looks like it would be faster if you were used to it.
There are, by the way, two other free IMEs, Google, https://www.google.co.jp/intl/ja/ime/ Baidu (yahoo!): http://ime.baidu.jp/type/ I consider both of them to be substantially better than Microsoft. Baidu's handwriting input is the best of the free IMEs (important for those times you can't pronounce a character but can write it), but google has been improving.
There are also premium IMEs that cost money but I've never bought one.