A mod worthy of getting in the top is those who count for all the components that make up a good game. That means original design. game play, community, innovation and least but not least - getting people to play and like it.
you can hop on to CGtalk, DevianArt, Polycount or any of the other hundreds of digital art forums and find incredible quality, but can people use it? No, and that is why they arent great games.
Moddb winners are mods who care about the whole package, it could be that some 16year old dude designs an Unreal mod that just captures everybodys mind and heart and wins the whole thing, even if the "quality" is crap. or like Minecraft, they deserve to win because they did what no one else did.
MOTY is fair, the best mods win, and best is measured by how many people like it, nothing else.
To use a cliché "It is not about the idea, it is about the execution" people look at screenshots of mods and go "bah, what's that, I could do that", but did they? No, they didn't execute on their idea, and that is why they don't have a mod.
So you can never say "They dont deserve to win" because if they do, they do.