I think Japan is one of the most versatile (and underrated) civs, but for different reasons than mentioned above. They get five bonuses - two of which are garbage, one of which is very good but comes a little late, and two bonuses that are very good and early. The two bonuses that are good and early are what I base my strategy on:
garbage bonus #1: combat bonus on coastal tiles or on the coast: just disregard this bonus. You'll drive yourself crazy trying to snare opponents (especially humans, but the AI as well) into fighting in specific tiles so that you get a very minor bonus, and probably sacrifice more successful tactics in order to get this minor bonus. If you try to take advantage of it, you'll probably be worse off than if you had just ignored the bonus.
garbage bonus #2: samurai: these units were lackluster before the last patch which buffed swordsman, and are now a complete joke with the swordsman buff. Their major flaw before the patch was that they don't upgrade from anything, and still don't - they're not like Roman legions, for example, when you can upgrade 4 warriors to legions on the very turn that you get them because nothing upgrades into them. Now that swordsmen have been buffed, they're a complete joke: they're only 12% stronger but nearly 100% more expensive and cost 50% more in maintenance. They also have a pretty short lifespan as the technologies leading to muskets are often higher priority than military tactics. I guess their bonus of fighting at full strength makes a nice nod of the hat to civ5's Japan, but is nowhere near enough of a bonus to compensate for the high production and maintenance cost. Seriously, if you have iron, just make twice as many swordsmen instead.
good but late bonus: electronics factory: it comes a little late to factor in to your game strategy, and (along with Germany) is one of the biggest losers from the first patch where area of effect districts no longer stacked. However, it is still a significant bonus. The common, every-game, default strategy is to ensure that all of your cities are covered by one factory's AoE production bonus, and in the case of Japan that means one extra hammer per city. A larger part of their bonus, though, is the +4 culture that you get when discovering electricity, a tech that is not that much further than industrialization. While the culture does not extend to all cities like the production does, it's the equivalent of adding two more monuments to each city that has the building, and this can really help in a number of ways. I wouldn't modify your strategy to emphasize this bonus, but rather just let it be a nice, passive boost in production and culture to your normal strategy.
great, early bonus #1: extra adjacency: You could go with the above mentioned strategy of cramming cities as close as you can, and that may pay off. I prefer to have a little more space between cities (well, just one more tile), and that works pretty good as well. The basic adjacency strategy (aside from district specific bonuses like commercial hubs near rivers and industrial zones near mines) is to have them form a triangle like farms with civil service. In doing so, each of the three districts is adjacent to two other districts and gets a +1 bonus for doing so. In the case of Japan, however, this is a +2 bonus per district. Furthermore, to build on the triangle another civilization would have to add two districts to either side of one of the districts in the triangle's "corner," which would result in the two new districts getting a +1 bonus, the district in that corner getting an additional +1 bonus (+2 total) and the other two districts being unaffected (total of +3.) In the case of Japan, though, adding on to the triangle in the same way would add +2 to each of the new districts, +2 to the "corner: district, and +1 to each of the original, "non-corner" districts (total of +8.) This is particularly beneficial with culture from theater squares as they have difficult adjacency bonuses, and the bonus is nice way for Japan to get a little bit extra in many categories (beakers, faith, culture, gold, and hammers) which is one of the reasons why I consider Japan a versatile civilization.
great, early bonus #2: 1/2 priced districts: Japan gets encampments, holy sites, and theater squares at 1/2 price. Most people seem to react to this advantage by saying, "grr... wish that was commercial hubs or industrial zones." But there is a good reason why these three districts were chosen: they are three out of the four "victory condition districts." If you're going for a religious victory, you'll want a lot of holy sites, probably one per city. If you're going for domination, you'll want a lot of (commercial hubs, I mean...) encampment districts. If you're going for a culture victory, you'll want a lot of theater squares, probably one per city. If you're going for a science victory, you'll want a lot of campuses (which Japan doesn't get a bonus to, but...) That means that 3 out of the four victory condition districts are 1/2 priced, which is a big bonus if you're going for any of those 3 victory conditions. The way that I use this bonus is to start by NOT making a lot of these three types of bonuses. Build campuses and commercial hubs early, while they are cheap. Get your infrastructure in place and a decent tech progression (getting you to electronics factories sooner.) See how the game plays out. And when you decide which is the best victory to pursue, the associated district is 1/2 cost.
Only with regard to spelling out the +5
