so my weeb ass is finally going to Japan. Main things me and my partner want to do are Ghlibi museum and theme park, see the life size Gundam, and go to a baseball game. We'll be mostly in Tokyo and Kyoto and then the Ghibli theme park in Nagoya. We like all the nerd shit so we'll be in Shibuya, Shinkuk and Akihabara, and maybe do some fancy stuff in Ginza.
You beat me to the recommendation, dammit. Enoshima Island is great. Extremely scenic and a recommended spot for couples. If you have time there, I'd also recommend looking up the Great Buddha of Kamakura (aka Daibutsu) and walking there, letting the whatever cellphone mapping software you use guide you. It took my partner and I through some very relaxing neighborhoods.
I can't stop geeking out over how good the Shonan Monorail is. It does what most monorails fail to do, which is to do things a regular train cannot. Steep hills in minimal space, single tracks with passing loops, it does it all and monorail was the right choice for the line.