Let's all just be glad for those exceptions. If they were written わ、お、え、 Japanese would be a much uglier looking language
hahahahaha. you're totally right.
as for the question about the particles, when you're new to the language these 3 exceptions seem kind of perplexing, especially when you know your looking up (at least) a 2000 kanji mountain. but in no time you'll adjust. getting used to this won't take much effort.
and you'll be surprised how few exceptions to the rules there are in japanese!
ganbatte kudasaaaaaaaaaaaaaai!