That's true.

However, if the supposed motivation is because somebody is suffering...why wait another day, another week, another month, another year?

If this took place before the election, you could call it a principled decision.

If this took place immediately after the election, you could call it a cautious-but-nevertheless-sound decision that might have otherwise been passed on to a (presumably friendly) successor.

Instead, this has taken place three days before he leaves office.

Manning hasn't gone anywhere in seven years. This was not based on a long bout of soul-searching or a sudden new development.

This was a move to either bolster Obama's legacy, or grease the wheels for a post-Presidential opportunity.

I'm not privy to the internal motivations of the President (or anyone else for that matter), though I can think of at least one reason besides the two that you've listed: doing so earlier would have made the issue that much more of a political football, principles aside (which is one reason why pardons and commutations are left for the end). I fight against being cynical as a rule. I'm not going to go out of my way to argue that this decision was made purely on principle. That said, it doesn't need to be purely craven posturing either.