Based on the adult game by Syrup: Many Milk.

What are some differences between Japanese life as usually depicted in anime VS real life in Japan?

People have made some interesting points already.
After years of watching anime I went to Japan (again) recently and the difference between real-life Japan and Anime that stuck me the most were: School uniforms. This is what Anime school uniforms look like: Found on http://anime-comments.blogspot.d... And this is what they really look like: Image taken from The mother lode of gakuran In short, there are only two types of school uniforms: Sailor Style (on the left in the above picture): Girls wear a uniform with a Sailor collar and a ribbon on the chest + a skirt in the same color; Boys wear Gakuran, a black, high-collared jacket with big golden buttons + pants in the same color. Blazer style: Girls and boys wear white shirts combined with a blazer.
Boys wear pants, girls a skirt.
Around the collar, they wear a necktie (boys, sometimes the girls too) or a ribbon (girls only). There are variations, of course, but they are not huge.
The dominating colors are different shades of dark blue and black, set off with white.
The only colorful thing is usually the ribbon/necktie which you see in darker shades of green and red, in light blues, and with patterns (mostly stripes) out of these colors.
The only other color you'll see are shades of ochre or light brown, but only on pullovers or cardigans. Some Sailor Style uniforms have a white shirt for the girls (only the collar and the skirt are blue), just like in Sailor Moon.
Some include a pullover or cardigan that is worn so it doesn't cover the sailor collar.
The Gakuran is really always black. Blazer Style uniforms feature different patterns for the skirts / pants, usually vertical and horizontal lines that intersect.
Often, the ribbon/necktie has the same color and pattern.
Sometimes the skirts have a pattern and the pants don't, but they usually have the same basic color (e.g.
the pants are grey and the skirts grey with a black pattern). Sometimes, the skirt/pants are a different color than the blazer, usually this comes as a combination of navy blue blazer and light blue / greyish pants/skirt.
Some include a vest worn under the blazer (same color as either skirt or blazer), some a sleeveless pullover that replaces the blazer in spring/autumn. Of course, in summer, students don't wear the jackets.
Most students just wear a short-sleeved shirt + pants or skirt then.
And a lot of (male) students wear their favourite T-shirts under the shirt, which usually shines through the thin white shirt fabric. Even if there are some uniquely colored school uniforms, I'd estimate that 90% looks just like that.
Even for more unusual coloring, you wouldn't find pink or violet or bright yellow on real-life school uniforms. Two additional things that Anime doesn't depict: 1.
Many students wear oversized uniforms.
Uniforms are expensive, and within the 3-year period a student usually spends at the same school (junior high / senior high), they could grow out of it.
So less wealthy parents buy their children a uniform that is one or two sizes bigger than the size they need when starting at that school, making sure that it will still fit 3 years after even if they grow. 2.
Schools tend to have very strict rules about skirt lenghts.
I think most schools require that the skirts should end shortly above the knees, some might even require that the skirt covers the knees.
Students do find ways around it, like pulling up the skirt and fixing it with a belt so it looks shorter, but I think you wouldn't find a school where the standard skirt only covers the upper half of the thighs. The last thing I have to mention: Some anime feature heavy customizations of school uniforms.
Something along the lines of: individual ribbon color, longer (!) skirt than everyone else, additional frills, shorter sleeves, pants in the color of the usual girls' skirt and so on.
Some also feature totally different uniforms for special students like the student council members.
As you can probably easily guess, all this defies the original purpose of a "uni"(=one)form, so it doesn't occur in reality. Of course, some anime depict school uniforms in a realistic way, but if you ask me, those are the minority.