Bread just isn't eaten that much in Japan, so obviously it's not as good as in Romania (which is once again far behind bread from Germany or France). Cheese is another product that just isn't quite as popular in Japan (in most of Asia for that matter, which is probably due to an overall much higher percentage of people with lactose intolerance) and doesn't have the same history and cultural significance cheese and other milk products have in Europe.
The sushi you get in Japan (and many other fish dishes for that matter) is far and beyond anything you could find in Romania for comparison, which is once again because fish just hasn't played the same important role in the history of Romanian food.
Yakitori is maybe something you can compare, because you find a lot of grilled goods at corner bistros in Romania as well and usually the quality in Japan is far beyond what you can get in Romania.
Ultimately what I'm getting at is that most countries probably excel at some foods and not at others. The further they are apart geographically and culturally the harder it gets to compare them I think.
It is very unfortunate that you found sake (nihonshu is what it is normally called -- sake just refers to any alcohol in Japan) not to be of your liking. There are thousands of nihonshu producers in Japan and the flavours range really dramatically. It can be sweet or dry, fruity or flowery. Not everybody likes it though.
I've never had Romanian beer, but I have heard that it is excellent. Japanese mainstream lagers are better than most mainstream Euro lagers, but not by any great margin. The higher quality mainstream lagers (Suntory The Premium Malts, Ebisu, and Kirin Ichiban Shibori) are all decent versions of German lager styles. Suntory has a cheaper "Malts" brand which is actually quite a good Munchner Helles IMHO. But as you say, it's nothing to write home about. Ji-beeru (micro brewery beer) is where it is at, but the movement is still in its infancy. There are many, many really excellent hefeweizen beers, but microbreweries are mostly concentrating on crazy styles.
Pickles... Don't get me started on pickles :-) Japanese pickles are awesome. They are also really regional, so if you are interested in pickles it pays to travel around to many small cities to try them. It's kind of unfortunate that many of the best pickles are quite hard to buy, but you should be able to get a decent variety at various omiyage shops.
If you come back again, it helps quite a bit to travel outside of the big cities. For example, it is really unusual to spend more than about 700 yen (7 US dollars) on a meal at a restaurant around where I live. And there is no tipping. Like many places in Europe, the best food is often found in the izakayas (bar/pub). In these places you eat otsumami (finger food???) while you are drinking. Apart from formal meals, this epitomises Japanese cuisine in my mind. The main things you will find are sashimi, yakitori, grilled fish, deep fried everything, and various kinds of stews.
It's really unfortunate, but it's quite difficult for travellers to experience the cuisine of Japan without having a guide who knows the area. I suppose this might also be true of Romania!
I live in Romania. By comparison, Romania has cheaper food, and much of it is tastier, including: meat, and especially smoked pork meat, cheese - you have to taste Romanian cheese from the mountains, it just doesn't compare to the poor examples of cheese I found in Japan. Our breads are 100 times better, you can find anything - long, short, round, crunchy, fluffy, with brown flower, multi flowers, seeds, anything really, except the Japanese originals: "mellon bread", "curry bread" and "anpan".
Bottled water tastes better in Romania, but Japanese tap water is amazing (never seen such good tap water, I drunk from the faucet). Romanian beer is much tastier too - I suppose it's because of better water. Wine - well, Japanese wines from the market are bad, and expensive. In my country I can find wine tasting 10 times better at a quarter of the price. Sake - I tried it but I don't like the taste much. Pickled vegetables - well, I would say we're even on this domain - Japanese have their own, pickled ginger and such, Romania has its own, usually cucumbers, peppers, cabbage, cauliflower and mellon (so tasty, pickled mellon).
So I'd give Japan a good grade overall, the food is tasty but different, mostly rice and noodles, very expensive, and in many domains lacking by comparison to food I know from my country. What I liked the most are - bento boxes, udon, mochi daifuku (very interesting tactile sensation), sushi and tempura.