What Makes a Compelling Leading Man?
E. Daniel Arey, one of the creative directors at Naughty Dog, posted a comment on Gamasutra about what makes a character compelling. While Nathan Drake is certainly one of the most likeable and fun to inhabit characters in recent memory, he is not the only such example.
Developers frequently look for ‘the way’ to do things, and those superior mechanics become codified and grow stagnant as effort focuses on perfecting identifiably flawed elements of a game. The protagonist, on the other hand, has resisted being pinned down in form or structure, and there seems to be no real push towards consolidation.
Whether a cipher, open ended or well defined, it is not the character that makes a story, but rather the opposite.
He was the strong, silent type
For a while it seemed that the silent protagonist was going to become a hallmark of immersive narrative-heavy games. This was largely because of Gordon Freeman and the unprecedented success Half-Life had in fleshing out a fabricated world for the player to explore.
In comparison to the increasingly gaudy ‘personality’ of Duke Nukem or the DOOM marine, Gordon Freeman was a fully realized and believable character. This was largely because he said nothing and therefore couldn’t trip up over his own shoelaces, but it was the first time developers realized that a little imagination on the part of the player goes a long way. All they had to do as developers was get out of the way.
It’s not like it’s an MMO, however, and you can’t just become anybody. The traditional silent protagonist is defined the by reactions of the players around them. In Half-Life 2, no matter how much you might want to, you just know Gordon isn’t identical to Duke from Duke Nukem given the way others react to him. Barney likely wouldn’t react the way he does to a god damned sexual tyrannosaurus like Duke, at least Alyx wouldn’t.

Gordon Freeman's ability to speak was actually lost in a tragic machinery accident as a child
Choose your own adventure
Silent isn’t the only open-ended approach. Take a game like Dragon Age; you choose your responses to characters and they react in kind. While the story isn’t scripted, and you get to choose the method of progression and flesh out a character; it will still be a reflection of your personality.
While some players might choose to play in a manner completely against how they behave in real life, there will always be some similarity there based on what you find amusing or how you wish you could act.

You can just see the character oozing through. Character's the skeleton guy, right?
This is what I would consider the middle ground, in which the player can invent a personality of their choosing and combine their imagination with that which the developer has constructed, while simultaneously giving the character direction and choices that focus the story on their personal preferences.
If every dialogue choice is tedious and boring the player won’t have much fun. Similarly, when a game like Dragon Age treads fairly familiar fantasy ground, it’s still enjoyable because the player can inject themselves into the action.
Along for the ride
The final compelling character archetype is that of Nathan Drake: the independent actor. Sure, you might have control of the protagonist during mindless action sequences, but when the plot pops up you’re merely along for the ride. You don’t control Drake’s actions, dialogue or choices.
What makes the story work in this case is that Drake is such a lovable rogue. You can’t help but identify with his predicament and easily insert yourself into his persona. Much like Indiana Jones or Han Solo from which he is based, it’s not hard to convince the player to pretend they’re Drake; who wouldn’t want to be Drake?

Alex Mercer: Fail
It’s clear that character types across the spectrum can result in great games, whether fully silent, a guided experience or an on rails narrative. Where developers go wrong is in choosing the wrong character type for their game. Would Gordon Freeman have been much fun to play in a game where you do laundry alone? Probably not. I don’t know if even Nathan Drake could make ‘Laundry Invaders 3000’ fun, but at the very least he’d have some amusing quips.
If the story is the strength of your game, then allow the player to experience it on their terms, and choose an open ended protagonist. If, on the other hand, the game is fun for its mechanics and set pieces alone, then make sure your hero is interesting regardless of what he’s doing. Otherwise you could end up with Prototype, a bland story with a bland character.