I had a similar thought with customization, actually. Link can still look like himself if he's decked out in new clothing or armor, and it's not like previous games haven't let you swap his clothing out before. If Link is supposed to be a connection to the player, increasing customization only enhances that. Perhaps this could be taken a step further by having players keep an eye on the environment and garb themselves appropriately, like warm clothing for snowy locales or dressing in clothes of a certain color to camouflage themselves in stealthy areas.
What I'd really like to see is overhauled enemy design and player combat. Enemies have been dancing around us for too long; it's time to have them constantly swooping in and attacking (with smart and fair design, of course), driving players to the limits of their skill in the trickier parts. But as Link's combat system is, however, this can't happen without being brutally unfair. Link just isn't designed to handle all that. Which is why I suggest three things to build on Link's combat system: more realistic strike impacts, advanced sword skills, and advanced dodging. No, I'm not suggesting Devil May Cry or God of War, but rather something pretty unique.
"Realistic strike impacts" is easy to explain: when you attack something in real life, your goal should be to drive through it and break it. If your attack bounces off, you were never intending to go through it, even subconsciously, which indicates sloppy combat skills. If you know what you're doing, your attack will either go through/push your target if it's successful or stay in place if it doesn't. Compare this to Link's sword always awkwardly bouncing off hard objects, and you'll see why Link needs to change his mindset - to quicken combat.
"Advanced sword skills" goes beyond the Hidden Skills of Twilight Princess, though the concept is generally the same. Although not all my data is intact, I've decided to pull one example from the upcoming Metal Gear Rising: Revengeance. To block and parry attacks in that game (I believe), you move an analog stick in the direction of the incoming attack, then press a button with good timing. Why couldn't Link do something similar? It would give him just a brief second to go in for the kill, and it would require skilled observation of the enemy. There are other skills too, like slower but more powerful two-handed strikes, slashing while getting up from a roll, and blocking attacks behind him. It may be better to save some of these as Hidden Skills so players aren't overwhelmed at the beginning, but giving Link more control over combat is something I'd really like to see.
Branching off that concept (can you tell I've thought about this before?) is "advanced dodging." Right now, Link just has side jumps, awkwardly shuffling to the side, rolling forward kind of slowly, and back flipping. What if we extended this to include more maneuvers like ducking, taking a quick step to the side, rolling after side jumps, rolling to your feet after getting knocked down, etc., etc.? It should handle pretty simply: by locking onto an enemy and moving the control stick to the side, you walk sideways. By doing that and pressing A, you shift your body quickly to the side. By pressing A twice in quick succession, you jump/roll that way. By locking on and holding the control stick backward (or maybe forward) and pressing A, you'll duck; twice in succession makes you flip. And when an enemy knocks you down, similar to Super Smash Bros., you press A with good timing and use the control stick to roll to your feet instantly.
But yeah, long story short, combat could use sprucing up, and I hope they do a moderate-to-heavy overhaul of it in Zelda Wii U.