Toyota's decks are awful. They sound veiled, closed in, muffled, and on and on. I own a Highlander and my wife owns a Corolla.
I bought an Alpine deck and iPod cable for my Highlander for about $200 or so and haven't looked back. Still have the stock speakers and have pretty good sound, so that tells me it's the head unit.
The Alpine deck was by far the best $200 I've put into the car. Crutchfield is pretty good with supplying instructions, adaptors, and so on. Makes it idiot proof. I've bought from them several times in the past. They have an 800 number to call if you're stuck, although I haven't used that due to the simplicity of their instructions.
I've had the Alpine for about 6 years without a hiccup. My brother went through a ton of different decks in his car until he got one. He's been very happy with one for about 8 years now.
If $200 is more than you thought you should spend, save up a bit longer for it. Trust me, it's easily worth it.
Sorry if I sound like an Alpine salesman. Just a happy customer. I know a lot of people with them, and none have ever had a problem.