What do you want? I think BESM [Tri-Stat] is far and away the better of the two. But it's also less crunchy, less "realistic", and less D20 System than BESM D20.
Frex, in BESM your basic combat values are calculated equally from all of your stats (though you can modify them in any number of ways, both broadly and for specific circumstances), meaning that the person with high social and mental stats is potentially just as effective in physical combat as the person with a really high physical stat--even when using a sword. It's a great match for a lot of the kid-oriented anime out there--or even just the frequently-seen idea that a pissed off person is just as deadly as a trained person. BUt it might jar with your idea of "realistic."
BESM D20, in contrast, is not only more realistic than BESM, but generally more realistic than D&D3E.
I really find it a bit weird to think of them [BESM & BESM D20] as being the same game, different core system, because they feel so different in the end. Really, i think they accomplish significantly different things. BESM D20 is an awesome implementation of D20 System, doing a good job integrating point-based and class-based character construction, and providing a much more free-flowing combat system than most other versions (with the notable exception of M&MM, and maybe others). It's very versatile and flexible, and adapts to a variety of genres with little or no work.
BESM is a fairly-rules-light game that is focused around a collection of anime sub-genres, and can do double duty as a mostly-universal game system.
So, if tying into other D20 System books with little or no effort is necessary, or if you just want point-based D20 System (never mind the anime), get BESM D20. If you specifically want light-n-fast or maximal anime, get the original (or, at this point, perhaps wait for BESM3, due out next month, i think).
