Cross server arena isn't an issue. Requiring players to reach 6 paths at least once in a 0 sum game, on an un-even battleground is a problem. The vast majority of players who have not reached 6 paths before 2.0 has no chance of ever reaching it for many months. Removing point loss for people who never reached 6 paths before would solve this issue effectively.
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Cross server matsuri isn't an issue. The matchmaking mechanism is in need of work. Currently, only one player need to be in the que for 60s to have random matches. Requiring both players to be in que for 60s for random matchmaking would fix the frustrating issues of meeting someone 30k+ pow higher the moment you press fight.
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The choice of server mergers is a serious issue.
A bunch of servers that got merged does not really need it. Their events barely run, but still do run even before the merger. When players in these servers become cannon fodders post merger, ofcourse they won't be happy. They are worse off than before the merger.
Many servers that desperately need mergers are not being merged. There are servers like mine, who has no sage/gnw/plunder for well over a month. I can count on one hand how many active players remain in this graveyard. Yet, time after time, my server did not get merged.
Players are not satisfied with the merger process because too many servers that need mergers do not get merged; while not every server that did get merged even need one in the first place. Actually merging completely dead servers, instead of sending semi-active ones as fodder to older servers would make players that much happier.