Answer: There are many different things you could use as a focal point. You could use a mugo pine or other evergreen, a small tree such as an ornamental cherry or plum or crabapple, a large stone or grouping of stones, a stone bench, an ornament such as a Japanese style lantern, a small garden pond, a small bridge over a "pool" of gravel....
In Japanese gardens there are usually very few flowers, if any. However you could add Japanese or Siberian iris, peonies and possibly some of the smaller, extra hardy rhododendrons in sun; moss, hostas, ferns and tricyrtis in shade and still have an Asian theme. If you are willing to go somewhat non-traditional you could also add cranesbill, ornamental grasses, sedums, and mums for example and still maintain that Japanese garden feel.
I hope this gives you some ideas.
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