wow no mention of Fatal Frame 4 :(
Actually, we're probably not missing much. Idiotic controls (they ignored the IR sensor and instead used tilting up and down and
turning the flashlight and your camera),
game breaking bugs, and terrible hit detection. I forget whether this is speculation or not, but I've heard Nintendo wanted Tecmo to clean up the problems (and implant IR control I think), but they didn't care to have the effort done so the game won't be published.
However, I doubt as good of an excuse will apply to most of these other games, but it IS good to keep in mind how much of it may not have been all that great afterall.
They're sorta doing that for games like Cave Story and La-Mulana (though I don't know if there's any compensation going around for the translations, especially since they received fan-translations years ago). Also they're getting buffed up for release on WiiWare rather than just getting a straight port.
Actually... that also doubles as why they aren't simply doing this for the fan translated game, it's still an amateur effort. Failing all else there would be the lack of creator input pointing out what was done right/wrong, note how games like Final Fantasy V received a much better localization (for its second release anyway) than the fan effort. SE may prefer skipping on a VC release in favor of a proper re-release with a quality translation.