It's a game...
The idea behind the game is to allow people to go through the motions of playing along with their favourite songs. I'm sure if it were so realistic that a guitarist of 40 years would find their real-life skills utilised, the rest of the non-musician population would be alienated.
I play the guitar, have done for 7 years. I also play the drums. I had a go on the drum version of the game in the US and lo and behold, being a drummer gave me no head start on the 8 year old who tried it out after me in the shop. And that's exactly how it should be: it's a game.
Do you need to be a racing driver to play Gran Turismo? Do you need to have been in the SAS to appreciate Call of Duty? No. The purpose of computer games is to give you the experience of some activity without actually exposing you to all the (often) gory details. If the author of this article would prefer a game with the challenge "hit all the notes in the aeolian mode to continue!" then he should write one, and see how it fares against GH3; not well, I'll bet.
In any case, don't worry that your guitar skills aren't immediately transferrable to this game. I'm sure that by following the same logic, you can also immediately play the bass, banjo, sitar, ukulele, or kantele. Go for it.