You "enter" the tourney knowing how it's going to be played - it you don't like it, then don't attempt to enter . I'm not disagreeing that I think it's unfair to the upper bracket winner, but more times that not I think it works out that the loser's bracket team doesn't move on as you run out of arms. Those two teams could play 10 times with a 5-5 record. I doubt either would have defeated Japan this year though. Mexico was pretty tough too especially considering their trip through the loser's bracket and all the pitchers they used.
People complained that pool play was unfair - especially a tie breaking system between three 2-1 or 1-2 teams and some gamesmanship that could be employed by a later game to ensure a team loses out on the tiebreaker which IIRC was some sort of runs against that perhaps included averaging innings played. So a modified double elimination is employed and that doesn't work either. I don't recall reading anyone complaining that the Legion WS played 7 inning single elimination in their semis/finals after playing 9 inning pool play games beforehand (admittedly I didn't read those posts as closely though ).
If it weren't for TV one wonders how popular LL would be. Doubt you'd see any 13's still playing. It is what it is - entertainment.... Thankfully they don't employ the electronic eye strike zone!