BO3 with map veto leads to some nice thinking and strategy. I like this part a lot : when you've spent a month playing the same guys, you have an idea of the maps they like, and the map they struggle with, so it adds some extra interest in having this system for a league tourney. It would be very sad if this interesting part was removed or reserved for the winner bracket. As an underdog, knowing that you will only play BO1 on maps you don't like, and then spend the rest of the tourney watching the best players on twitch ... not very thrilling.
Moreover BO1 raise the problem of : how do you chose the map ?
It's clearly a matter of waht do we prefer : BO3 but we meet less players, or BO1 where we meet all players.
Maybe some hybrid combination is better : keep it swiss style but we start with few (2,3,4 ?) BO1, which serve as "placement matches" where we can meet anybody, and then we have ... let's say 2 BO3 against players with similar results. That way we keep the best of both worlds.
Initial pairing according to league results adds the possibility of meeting some much better/worse players in the first round. I liked this, because I would never play the top players otherwise, and the tourney would just be me facing my usual ladder opponents. That's why I suggested above that the first BO1 would be "random opponent", that way during the placement matches, we can have unusual matchups, and then for the more "serious part" with BO3s we have an opponent of our level.