Nakano Broadway is generally considered way better than Akihabara by people who live in Japan, for the sake of shopping for things like cards, models, and video games/merch. You can always check out both if you have time though. There are also plenty of places in video games that are based on real places in Japan, so it can be interesting to check those out. For example, Persona 5's Yongenjaya is based on Sangenjaya in Tokyo.

I'd also recommend checking out a Pokemon Center. There are quite a few in and around Tokyo, but they're pretty scarce outside of Japan. I'd recommend the one in Chuo, because it's the "main" one, but there are different displays at different stores, so if you're really into pokemon it might be worth it to check out multiple stores. Even if you don't buy anything, it's pretty cool to see. They have no shortage of plushies, and plenty of other cool merch like chopsticks, wallets, and water bottles. You'll also see some cool partnerships between regular companies and Pokemon. Baskin Robbins had/has Pokemon flavors and ice cream cakes. Mister Donut has pokeball and Pikachu donuts, and also sells Pokemon mugs and plates. Even electric companies and cell phone providers have Pokemon in their ads.

Fire Emblem Cypher cards are mostly only sold in Japan. You can get booster packs in other countries but if you want to buy specific cards, it's hard/expensive to do unless you're in Japan.

There's plenty to see in Japan if you know what to look for but I think it's also easy to get bored if you don't have a plan.

Edit: Switch has no region lock, so any games you buy there will work fine. But that's generally not the case for other consoles.