Girls having Double D boobs like in most of the anim-
oh wait.. Already been to Japan, dream crushed with a bunch of mini a's.

Not even capital A.
Just a.

perverted girls who are easily swayed by the simplest heroics of a guy.

Food

This is one of the most likely things you'll find in common with anime which physically takes place in Japan.

As I've been to Japan several times already I cannot say what I think is, but I'll try my best at pointing out some things I've seen in anime which are quite close to reality in daily life.
Minor things I have noticed while traveling through Japan which I've also seen in anime are people sleeping on the subway (very common), salaryman in Izakaya (Japanese pubs) and their quite typical behaviour (extremely common), morning and evening commutes (Avoid, AVOID! No seriously you do NOT want to be in a train during those!), Shibuya crossing (people, people everywhere!!) and back when I was a smoker myself, Japanese smoking habbits.
(Most Japanese people I've seen smoking never finish a whole cigarette, they smoke half or take a few puffs before extinguishing it and moving on or lighting the next. In a lot of anime with smoking characters the exact same happens. I was the one getting weird looks, well because I was a big European foreigner of course, but also because I finished the whole cig. )

Check out my new web show and blog about all things Japan www.kawaiistudyjapan.com! Check it out on facebook too! I've been working uber hard and just launched so I want to spread the word. First episode launched TODAY YAY! After you watch that episode you'll see that I talk about this topic already a bit even!

Super natural powers~!

The cosplaying cafes. :3

Oh man! I really hope that the festivals when people wear yukatas and dance around a bonfire are the same!! and don't forget the burning kanjis in the mountains!!

Oh Oh Oh!!! I almost forgot!!!! that the cherry blossoms actually drop on my beer!!!

Mini skirts are a big thing over there so be happy :p

These pictures only feed my desire....