This sort of thing is why I hope publishers get phased out. It will be hard, as they've served as the gatekeepers for the video game industry for years and they won't give that up easily.
I am not an attorney nor do I have any legal training. In my layman's opinion though, they are technically and legally correct:MGS is their series. Publishers in any industry (save for possibly literature and technical writing) make a point to secure IP rights on anything they publish. Even though it was Kojima's idea and his name is attached to it, the series belongs to Konami.
This same thing happened with Mega Man and Capcom: the dev and Capcom had a falling out, Capcom kept the Mega Man name, and the dev had to start what was essentially a knock-off series of his own game. Iga is working on something similar with Castlevania, as well.
Now that digital distribution has become so widespread, and Patreon makes crowd funding these games a reality, I think more an more of the major series developers are realizing that they can strike out on their own and maintain absolute control over their IP rather than having to answer to a board of investors or listen to a committee. I hope this becomes the norm and more developers take this approach. Businessmen are smart people but they are businessmen, not content creators. They do not need to be telling developers how to do to make a game anymore than I need to be telling an electrician how to wire my house just because I sign the check.
I hope more developers use the internet to weaken the industry's dependence on a few publisher gatekeepers who seize IP rights to content they only helped fund and distribute and did not create. The internet has made it much easier for people to connect without having to have a formal organizational structure. Devs can connect with graphic artists, animators, musicians, etc. without having to be a part of a company to bring all these elements together. They just need the funding and distribution, which the internet can also easily solve.
