For Japan to become a colony requires a set of very early PoDs.
Basically, after the beginning of the Sakoku period it's incredibly unlikely and implausable.
Japan was not only a very unified society (sure their were Daimyo's carving out their own little fifes at some points, but they'd all fight together against a common threat) for most of its history, and especially by the late 17th century onwards, but also homogenous, so any divisions were temporary and power struggles, not attempts to break away.
Aside from that what resources Japan had were simply not worth it.
Another thing to consider is that Japan did'nt just magically industrialize when the Meiji Emperor took over, it had been modernizing most of the 19th century under the Shogunate.
Ultimately the one thing you really have to realize is that Europe's colonies were gained two ways;
-Colonizing an area with relatively low population.
-Having a large technological/weapons edge (only really applies from the 19th century onwards).
Their was a very good reason that the few colonies in East Asia were small and established after 1840, that being that East Asian society, was unified, had large populations and did'nt allow itself to allow the technology gap to become massive.