Proper Hepburn romanization (original or modified) wouldn't work well on MDL because it uses macrons, and I've discovered the body text font used on MDL dosen't support macrons, so they show up in a different font from other characters: e.g., oō uū aā iī eē when they're adjacent one can see appear with different sizes and weights. The differences are more noticeable when they're italic: oō uū aā iī eē.
MDL could therefore either (1) change the font or (2, which would be easier to implement) use circumflexes instead of macrons, which Hepburn allows when macrons are not available and is what IMDb uses, as the old text-encoding system it uses for Roman-character titles doesn't support macrons. Circumflexed letters do appear in the same font as unaccented letters: oô uû aâ iî eê oô uû aâ iî eê.
I would, if my voice counts for anything, also vote to use Hepburn romanization as the default, but with circumflexes, and specifically modified Hepburn (which is a bit more consistent, with less exceptions than older forms). It's not perfect (it doesn't distinguish between when certain subsequent vowels such as ai, ii, ei, and oi are pronounced as part of the same syllable or the end and start of different syllables in Japanese words), and other systems are more indicative of how the sounds are written in Japanese, but it's the system that is the most intuitive for people who know nothing about Japanese. Also, it's what other sites such as WikiMedia sites, IMDb, and Anime News Network use as their standard system, so it would make exchanging romanizations between those easier (though macrons would need to be switched to circumflexes and the other way around, and not everything on those sites follows their own rules, so they can't be trusted blindly).
Another big question is how to capitalize romanizations of titles. But as that is purely aesthetic and dosen't affect searching, it's not as important.
However, my opinion differs in that I would only use Hepburn romanization for real people and companies' primary names when no official Roman-character spelling or one commonly used by reliable/authoritative sources has been identified by MDL users so far. The modified Hepburn romanization readings should be given on all real people and companies' pages as a standardized guide to pronouncing them, and they should be entered as an aka for search purposes.