Snowden deserved Obamas pardon a lot more than Manning. I get the sense that Manning leaked stuff for the sake of leaking stuff, while Snowden uncovered a vast domestic and unconstitutional espionage program to which the general public was unaware.
NSA being an angry little child with a napkin aside, I believe there was a legal hurdle to Snowden being pardoned: You need to be tried & sentenced before a presidential pardon can be applied, as far as I understood.
Surprisingly, that actually isn’t required. Nixon was pardoned without even being indicted.