I love all the ideas mentioned for a museum! Archives, traveling exhibits, cool galleries, interactive displays. Yes to it all!
I’d love to create a stamp rally of some sort with Pokemon stamps lol. Maybe it can be like the Stamp Caravan that the Travelers Company (notebooks/stationery) does! So it would travel around the world to different card shops. 
And the stamp rally could, of course, also be available/part of the museum.
I’d also put some of the funds aside so I can travel back to Japan and visit all of the Pokelids. I’ve seen five in Yokohama, but there are a lot more to visit!
And of course I’ll visit the Pokemon Centres.
While we’re at it, host another E4 get-together - a portion of funds can be put to some great in-person events. 
And, finally, I’d like to see more short series like Pokémon Concierge, so I’d use some of the money to commission this as well. 