As for lethality: I recommend you use the lowered massive damage threshhold rule and increase the DC for additional damage beyond the basic (nods to Steve Palmer Peterson.)
At any rate, I prefer d20. I have never liked dice pool systems that rely on fidgety-combination convention exemplified by L5R (either edition.)
In addition, I think that d20 (ironically) offers more character diversity. In essence both are class based systems. However, in L5R, once you know the school of a character, you know most of the basic capabilities of a character. But in d20 you might know the character's school, but the character's classes and feats help create a totally different character from another character with the same school, depending on what base classes, prestige classes, and other skills and feats the character may have.
Further, unlike L5R classic, you can actually play a character who is not a member of the Buke caste... you could play a commoner if it suits you, or members of other races.
Finally, I am not so sure I agree with the sentiment of the necessity of lethality of duels. Sure, it adds a little edge to the setting, but I wonder if it does so too much. To me, character continuity is important in the game, and it seems that the level of lethality in duels makes a stark contrast between bushi and shugenja and other types of characters. Too stark for my taste.
And top that all off with the fact I think AEG did a bang up job with the Rokugan core book, which collects more game relevant L5R info in one place than any product that had gone before.