Day 1: west Yamanote
Shibuya Crossing → Meiji Jingu → Takeshita or Omotesando. Leave Shinjuku for another day, or close with the Gyoen. Do not chase Asakusa at night.
Day 2: Asakusa and the tower
Finish Senso-ji and Nakamise, then cross the Sumida to Skytree. Do not jam Ueno museums into the same morning.
Day 3: centre or bay — pick one
Ginza Yonchome + Tsukiji outer, or Odaiba seaside + Toyosu Planets. Doing both is a day on trains.