Two days covers east Tokyo and west Tokyo if you start at opening and do not stack them on jet lag. Three days is the comfortable minimum for Shinjuku recovery and Shibuya without treating the metro as the holiday.
2 days: east and west
Day one (if you are not jet-lagged): Senso-ji at 8am, Ueno, Shibuya evening. Day two: Meiji Jingu at opening, Harajuku, Omotesando, Shinjuku yakitori. If Day 1 is an arrival night, swap: Shinjuku recovery first, temples the next morning.
3 days: city plus neighbourhood
Keep the two-day core, then give day three to a slower Shinjuku Gyoen, the free Metropolitan Government deck, or Akihabara if that is the trip. This is the version that still feels like Tokyo rather than a station map. Hakone if you pre-booked a ryokan and still have legs — better as night four.
5 days: Tokyo and Hakone
Three city days, one Hakone overnight (onsen, Fuji view, kaiseki), and one buffer for jet lag. Stay in Shinjuku so you are not commuting across the city each morning. Then Shinkansen to Kyoto — about 2 hours 15 minutes if you booked Hikari or Sakura (not Nozomi on a JR Pass).
Build a custom version with the LokaTours trip planner. Pair the days with the 18 best things to do in Tokyo, the 15 best places to visit in Tokyo, and Best Time to Visit Tokyo if Ueno only makes sense in sakura season.