In general, I find your attitude a bit condescending. This is what I wrote about my choice:
> note i could also have used a different romanization that renders し as "si", つ as "tu", and ち as "ti" for this article. i decided to not because everyone else uses romaji, and once you understand this point once, you shouldn't have a difficulty doing this in your head
My main mistake seems to be meaning “[Hepburn] romaji” by writing “romaji”. I was obviously aware of other systems because that is what the sentence says but I thought it’s acceptable to refer to Hepburn as just “romaji” as a sort of the default one. Maybe that’s wrong.
Other than this terminology nit, I think I’ve made myself quite clear there. I genuinely don’t think it’s a big deal. Maybe I overestimate my readers’ intelligence but I don’t find this difficult to live with at all once you get it.
Roman numerals is a funny parallel but it doesn’t hold very well. The difficulty of using Hepburn is O(1) shortcut: for conjugation, you only have to “remember” three special cases and they’re always applied just-in-time. It’s just substitutions — and are arguably inherent phonetically. Arithmetic with Roman numerals requires many stacked adjustments where you have to match pairs of things. And lack of orders really screws with ability to do multiplication. This just isn’t an intellectually honest comparison.
Re: your last point I actually kind of agree. I’m that annoying student who likes to un-extrapolate backwards from examples to the rules, knowing which gives me a warm fuzzy feeling, after which I can go back to examples. My article is for people like me. Maybe there’s a few more of them.