They're both the same company, there's no reason for a distinction.
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@marino: Co. Ltd. is also used in Japan. NCL (the official abbreviation for Nintendo's Japan headquarters), for example stands for Nintendo Co. Ltd.
However, upon further inspection, it seems that there's a distinction between Natsume as a developer and Natsume as a publishing company with Co. Ltd. being used for the developer and just Natsume for the publisher. BUT Natsume's wikipedia article suggests that they're on and the same actually. Natsume IS Natsume Co. Ltd. Their only other branch is their North American publishing subsidiary, Natsume Inc. (also referred to as Natsume USA).
Thus, I'd say my original request seems justified by someone at some point should maybe make a Natsume USA page and tag their US releases with that name instead of the general Natsume company.
Btw, what is the preferred way of entering company names? Neutral, without the suffix denoting its business entity type? (Natsume vs. Natsume Inc / Nintendo vs. Nintendo Co. Ltd.) Because right now we have no consistency regarding this (non-US companies are often added with their business suffix, see CD Projekt RED Sp. z o.o. or 8-4, Ltd.).
@def: In the beginning, I remember Jeff saying something about not wanting all the suffixes. Obviously this hasn't become standardized and, in general, a lot of the company info is pretty messed up right now overall. It's something I've wanted to fix for years, but I simply don't have the time to do it. At one point we had over 20 different Konami pages and it's probably still too high. The suffixes just confuse people and lead to duplicates of the same development studios and/or publishers that only appear different due to a suffix that we could've just listed in the aliases. Hopefully I'll get to it eventually.
I'll delete the Natsume Ltd. though.