What to do with a 2.5 days stopover in Tokyo

Hi!
Mt Fuji is weather-dependent. Be ready to cancel if the chances to see it are too close to zero.
The remaining 1.5 days in Tokyo entail some tough choices; you certainly cannot complete the whole list in such a timeframe (or even 2.5 days). Here are my comments, hoping they are helpful. I am not a "Japan expert" but I am lucky enough to have been a few times.

• Sumo stable: you need a tour for those, I have never done such a tour. It seems time-consuming.
• Asakusa Senso-ji Temple and Nakamise: a lovely morning visit
• Tokyo National Museum: yes, great collections. Combines well with Asakusa
• Meiji Shrine and Yoyogi Park: Meiji shrine is atmospheric and worth a visit, but best combined with a visit to adjacent Shibuya or Shinjuku districts. If you have no interest in those areas, I would not trek across Tokyo just for it. As for Yoyogi Park, it is just a park.
• Mori Art Museum: never been. Interesting only if the current exhibit interests you. Check also Nezu museum, it is very charming.
• local craft center: There are many options. I liked Japan Traditional Crafts Aoyama Square and 2k540 Aki-Oka Artisan in my feb 2024 visit. The former combines well with Mori museum, the latter combines well with Asakusa / Ueno.
• Imperial Palace: you can only visit the gardens. I find them only moderately interesting.
• Yakata temple: could not find it
• Tsukji market/food tour: I had been when the market was still there. Now, it is no longer there; only food stalls remain AFAIK. Many of them! It could be fun as a tour, but I would not prioritize it

Thank you Balso! What would be on your list to visit? What would you prioritize?

https://www.tripadvisor.com/Attractions-g298184-Activities-Tokyo_Tokyo_Prefecture_Kanto.html

For Yakata temple - did you possibly mean walking around Yanaka, where there are several temples? I like poking around that area; it's a very different experience from Asakusa.

What to do depends upon your interests. I'd also recommend the Hama Rikyu garden, which is near Tsukiji if you want to see the shops there (the fish auctions are in Toyosu now). Strong second of Balso's recommendation of the Nezu Museum. Their garden is also nice. The Idemitsu Museum is in a skyscraper overlooking the Imperial Gardens and they have a viewing area. If you are otherwise interested in the exhibition while you are visiting, the Idemitsu also gives you another way to experience the Imperial Palace.

I feel like the canonical trip to Tokyo must include Asakusa, then add other attractions based on your interests and available time.

If Yakata is Yanaka, then yes, this is a great area to wander around.
In a day, you could easily start at Senso-ji, walk in the surrounding streets (Nakamise-dori with all the stalls, and the arcade that crosses it), pop by Kappabashi if you have any interest in kitchen utensils, head over to the Tokyo National Museum, and wander off towards Yanaka.

When will you be in Tokyo. Beware of the rainy season. If you are there when it rains, then have an umbrella ready.

There is so much to see in Tokyo. Do you want to see its modern side or traditional side? No matter what, a night visit to the famous Shibuya crossing is a must. You can go there around or after dinner time.

Bear in mind that Tokyo is a massive and sprawling city. It takes time to get from one spot to another, even with the subway.