It is an inherent fact of games that the player will identify with the play-character; the act of playing literally requires it. Perhaps, though, it's time to realize that creating characters to identify with and characters to empathize with are two hugely different things. Maciej Szczesnik, lead gameplay designer on The Witcher 2, made just this point to Gamasutra:
"I think that this idolization of the main character will not work...I think it's all about empathy, actually. It's similar to watching movies, right? If you can empathize with the main character, you will feel his emotions and you will be able to understand his motivations, and you'll be able to eventually understand the storyline, and you will be able to like it. And if you're not able to empathize with the main character, basically you're watching something."
There are different ways of creating empathy. Nintendo is masterful at drawing characters that elicit empathy through their appearance (Link, Mario). Rockstar moved from generic psychopaths (in Grand Theft Auto 3) - classic blank-slate avatars - to the real, shaded life of Niko Bellic in Grand Theft Auto 4. That, for me, was the game's crowning accomplishment. This, of course, requires careful writing and attention paid to storytelling, qualities that the industry does not have in abundance. Thank goodness then, for the BioWares of the world, who with the customizable but still idiosyncratic Colonel Shepherd, nailed a perfect mix of identification and empathy.