We ate at the Japan TS when it was the other name. I don't know how different it is now, but just to keep my comments in perspective...
These two restaurants offer two very different experiences IMO.
In Japan, you will be sharing a table with other people. Neither good nor bad, just something to think about when you picture your meal. The food is fresh and hot, cooked right in front of you. You end up eating your meal in stages a bit, eating as the food is prepared. Depending on the size of your party and if people order different things, this means that some food will be ready faster than others. Some may be eating while others aren't. This mostly affects younger diners, but isn't an issue if you share. The meal is more about watching your food be prepared. It is an entertaining meal. It is quite relaxing in a way to just sit and watch and be quiet for a while. I've rarely read negative reviews of Japan TS. I think I've read more about disappointment over the fact that they don't do fried rice than bad food.
San Angel Inn has very cool atmosphere. The tables can feel a little close. It's a dark, dark restaurant. I remember I could see my food better in my pictures than in real life. This had a quiet effect when we were there. It didn't strike me as a loud restaurant. Not library quiet, but I don't recall booming music or voices, etc. We could here the band playing in the common area at different times during the meal. I think the food here is hit and miss. My family enjoyed our meal here. Here's the link to my positive review:
http://www.disboards.com/showpost.php?p=20550900&postcount=51
IMO, as with all restaurant choices in WDW, it's not only about the food, it's about the dining experience. Which kind of restaurant do you see fitting into your day better?
I hope this helps to highlight some of the differences between the two.
