I've studied Japanese and studied abroad in Japan, so I'd definitely like to return, but it seems to me that the easiest way to do that would be by getting a job at a big company like Rakuten.
If you have a university degree, it is actually pretty easy to get a visa here. While you might have trouble getting a job at a 3-person startup, something a bit more established shouldn't be an issue (as the article mentions, Gengo recruits non-Japanese, and they'll even hire people who aren't already in Japan).
The easiest way to get a job here is the same as anywhere else: be exceptional at something that is in demand.
If you have someone who can help you through the paperwork, creating a company isn't so hard. It took us about 60,000 yen and one month to create at Godo-Gaisha (similar to a LLC).
I didn't actually do the paperwork, so I don't actually know how complicated it was. We're actually incorporated in Chiba, and at that time (Nov 2008), the government office responsible for the paperwork wasn't very busy, so they were happy to help out.
Unless you are fluent in Japanese, you probably will need help from someone else. If you don't have a Japanese cofounder / spouse, probably the best thing is to pay someone to help with it.