Thornton was a little unlucky with shooting percentage (3% below career average), and his teammates (at 5v5) on average were a little unlucky too (a couple percent).
Shooting percentage year-to-year isn't something players can control. Some years, everything they touch turns to gold (Corey Perry, Ryan Kesler), and sometimes it seems the puck is a foot wide (Ryan Getzlaf, Nikolai Kulemin). Obviously some players are better shooters than others, but for each player individually, their highs and lows are usually within a range.
The better or worse your "luck" is one year, the more likely it is to "regress", or move towards average.
That doesn't take into account things like injuries - Getzlaf and Kesler both had awful years, and both had a lot of injury issues. That's probably not entirely coincidence. That said, I'd take Getzlaf this year by a fair bit.
Thornton cause he doesn't have motivation problems, less likely to get injured and produce the same amount if not higher.
Getzlaf's apparent "motivational problems" are blown way out of proportion. Many Anaheim fans even think that last year, his worst production wise, was the year in which he worked the hardest.
And besides a sports hernia injury about 4 years ago, he's been pretty healthy despite a few fluky injuries (taking a puck to the face).
... and lastly, don't forget, this year is a contract season for Getzlaf. All of that, plus the fact that Getzlaf is a little younger (I'm not saying Thornton's regressing), I'd say Getzlaf is the better choice for this season.