According to the Nintendo online store the Pandora's Tower copyright is owned by both Ganbarion and Nintendo and The Last Story is owned by Mistwalker and Nntendo.
It seems to be the same situation that Nintendo has with Koei Tecmo, in which they both own half of the Fatal Frame franchise. Nintendo learned this approach from long time Nintendo partner Owe Bergsten who only ever buys 50% of a company so that they can be on equal terms rather than one ruling the other.
The rest is owned by Nintendo.
Right. Nintendos website mentioned the copyright being shared with Mistwalker. I failed to state that fact.
Their store never mentions trademarks, which is perfectly normal.