I don't think there's anything inherently wrong with the core mechanics of l5r, just with the cardpool. Since we're starting from square 1 in that regard, while I imagine it won't be backwards compatible, I'm hoping that not too much changes in terms of the overall 'stronghold, 2 decks, 4 provinces' structure.
As is Military will always be the on average strongest deck type, period, because its like a mixture of fast creature blitz + blue control to compare it to a magic decktype.