Japan was a one time thing. At first, CONMEBOL was supposed to have 2 regular guests, Mexico and the US. they participated in '93 and '95 but when '97 came around the US dropped out for good. Costa Rica became its replacement but CR was too weak of a country to participate every year. When '99 came around CONMEBOL had Spain in mind to be that year's guest along with Mexico but they could not get them to participate so they went to plan B, Japan. This upcoming year will be Canada's turn, a worthy opponent since they won the Gold Cup.
I think that in a few years, Copa America will have more than 12 countries involved, maybe 16 like the Euro Cup.
CONCACAF's Mexico, Canada, USA and 3 different guest for every year (1 from Europe, Asia, and Africa perhaps?), along with CONMEBOL's Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Paraguay, Perú, Uruguay and Venezuela.