I think solid B+ would be my rank here. For the most part, the contest was ran well. My rationale for not going to an A would be a few sticky points.
RE2/Bloodborne should have been postponed. We shouldn't be having matches losing two hours in a post-Mario/Crono world. It's not 2002 anymore, and we could have just taken a day from the break to align the schedule back to normal or something.
If there was a loose series cap, why? I appreciate the fodder, and I have found a lot of favorites due to the lower end of contests, but they shouldn't be coming at the expense of Skyward Sword, Super Mario 3D World, or Final Fantasy 13. The way this contest ended up going, they could have busted a lot of brackets in losing matches we wouldn't have thought possible. As good of a contest Persona 5 had, imagine it taking down FF13 in Round 2, cementing itself as the premiere JPRG series of the decade.
The break seemed like it was better handled this time around with more yellow notifications pushing Second Chance entry and such, but I'd still rather see incentive to come to the front page to keep people around that week. To the point where I actually switched from taking the RE2 upset to Mass Effect 2 in second chance because I felt that could be a factor. It worked out for me even though it turned out ME2 would have won by more actually, but maybe doing some exhibition polls featuring the worst of the decade would keep people habitually visiting the front page the entire time, and maybe resulted in less people posting in the Stats topics or the unrelated stickies topics wondering what happened to the contest.
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Agent Triple Zero at your service! This line reserved for the true greatone, azuarc, winner of Game of the Decade!