Seperating hybrids into its own category, as people have already mentioned.
Being able re-shaft irons/woods/hybrids/wedges seperately, as already mentioned. I hate putting with a graphite driver shaft just because I tweaked it for my driver.
More pro golfers, whether out of the box, unlockable or DLC - in last year's version there weren't enough golfers to properly make up the European or US teams for the Ryder Cup, same again this time for the President's Cup. If you're going to put in that feature, at least include enough European golfers to make up a European team, and the same with the US. I'd love to see the likes of Els, Donald, Mickelson, Dustin Johnson, or god forbid, the world number 1 & 2, Kaymer & Westwood. Having Danny Lee and Rocco Mediate, Boo Weekley - these guys are nowhere in the world rankings, who wants to play with them? Just load it with as many top 20/top 50 players as possible and its surely a better lure and marketing strategy. Getting the Molinaris, Rickie Fowler & Bubba this year is a good start - now drop the average guys and get in some more front-runners.
I'd like to see a build-your-own-swing feature (this was in the game until about 2007 I think) so if I create myself I can make my own swing. Other than Tiger they all have either a stock, dull swing or a crazy, zany one which EA are obsessed with where you drive one-handed or do a Happy Gilmore or something. If you're going to put those 'joke' things in, at least give some realistic alternatives too.
I'd love to see 'spin' come back as a stat - some players generate more than others, I know I get a lot more with my wedges than my playing buddies, which makes my short game pretty decent. But if I hit a 4 iron in at a green I can't stop the ball dead and spin it back 6 feet, it's just not possible unless you hit it up into the gods.
Last but not least (I know this won't happen because of the processing limitations of the PS3/360, and definitely the Wii), can you imagine a create-your-own-course feature? Even if this was a DLC thing, creating your home track, or a course not in the game, would be fantastic. And I don't mean, pick Hole 1 @ Pebble, Hole 2 @ St. Andrews etc, but actually placing a bunker here or there, a stream here or there. I understand this is also a licensing thing but they wouldn't be official versions and as it couldn't be laser tracked they wouldn't necessarily be close enough to the real thing to cause legal problems. I'd love the idea of duelling it out down the 18th on my home course against Tiger and Rory in a play-off. Sigh.