I don't know why there is such a big fuss over Mercy.
It didn't make the album.
Hell, it didn't even make the cut as the b-side to the first single (Are You Gonna Wait Forever and Neon Lights made it).
I don't doubt U2's wisdom.
But to me, Mercy is nothing but a ripoff of A Flock Of Seagull's "The More You Live The More You Love." Obviously, U2 don't want to put obviously and blatanty borrowed riffs and melodies into their released songs.
Mercy shouldn't have even been leaked in the first place. It puts U2 in a bad light.
So the answer is no, it shouldn't be put in the Best Of 2000-2010.
Cheers,
J