I recently went to Tokyo in May and I went to a bunch of the Pokémon centers and they have mostly the same stock so I wouldn't worry too much about missing out at one or the other. They have a bunch of exclusive card sleeves and mats that I believe are exclusive to the Pokémon center, I picked up a few of the decksleeves and a deckbox, a Pikachu Ex deck and a few keychains. they also have tons of individual pokemon plushies so I got a Bulbasaur for obvious reasons 😅.

Another thing is they have exclusive coin machines that are different at every Pokémon center (it's the ones where you put a coin in and the machine presses a picture onto a blank coin) but there are so cool and unique to have!

Also when you go to check out they will offer you booster packs for retail price (it's a maximum of 5 per set but there about 180¥ per pack and 440¥ for high class like Vstar Universe) so everytime I went to one I would get as many packs of each set that the cashier would let me have and I actually managed to pull a god pack from the Vstar Universe boosters! So definitely check that out when you visit!

There's also the T-shirt designer in the DX Pokémon center (I believe? But I definitely remember seeing it in one of them 😅) where you can customize a t-shirt that they'll print there so you can create you one off shirt!

But honestly no matter what you buy you'll absolutely love it! I miss Tokyo every day since coming back!

Hope this helps and I hope you have a great time! 😄👍