If you want to save on transportation cost, here's what I would group them :
Ginza, Tokyo Tower, Roppongi Hills - connected through Hibiya Line and Oedo Line
Ikebukuro, Shinjuku, Yoyogi, Harajuku, Omotesando, Shibuya - connected through Yamanote Line and Ginza Line
Tsukiji, Odaiba - connected through Oedo Line, Yurakucho Line, Yurikamome Line and Rinkai Line
To get optimum suggestion, it is best if you could tell us your travel interest such as theme park, fashion, religion, the different japanese-pop-culture, roller coaster rides, dining, shopping, night life, souvenir collection and etc.
Hi, thank you so much for your advices. i try to group the travel route based on my hotel location. On the first 4 nights, I will be staying at Ikebukuro & the following 2 nights will be at Asakusa. I got no any special travel interest, I just wana go to the places that I mentioned above & see Tokyo with my own eyes. Ya, I wish to see beautiful autumn leaves..can u suggest which is the best spot to see the autumn leaves? Thank you.