My parents own an 04 or 05 Highlander, and I've got to say it's really been a dog. I've always thought very highly of Toyota, but the Highlander has been enough to make me think twice about buying one anytime in the near future.
1st it's got a check engine light issue. The charged my parents a few hundred dollars to reflash the ecu to take care of the issue. Except it was back in less than a week. Now they say it needs new catalytic converter(s) and will cost $1100+ to fix. The car runs just fine however and doesn't leave an unburned gas smell like a non-functional catalytic converter would have so I'm not really sure if it's just them wanting to throw parts at the problem. Further, the problem sometimes goes away after getting gas, leading me to believe that it might be related to the gas cap which is incredibly funking on the car.
2nd it's got an air pressure monitoring system that sometimes just trips and you can't untrip without going to the dealership. That means anytime the air in the tire gets low, or the system thinks it is even if it isn't, you have to take a trip to the dealership because the method for reseting it doesn't actually work. They supposedly fixed that last time it was in the shop, but I rather doubt it.
3rd the heater doesn't work. More specifically, the heater doesn't work in the winter. You absolutely cannot get the heater to come on in the winter. However, if it's warm outside and you hit a bump it will come on regardless of where the dial is. Supposedly they fixed that this summer at the shop, except I've driven it twice this winter and been unable to get the heater to come on.
4th when you step on the gas, it doesn't really do anything. It's my understanding that this was one of Toyota's first cars that had the electric gas pedal. And while I'm certainly glad it doesn't just start accelerating like some of them have done, it presents it's own form of danger. You can floor the gas pedal, and it takes almost a full second for it to notice you've hit the gas. It seems slightly less noticeable when you're making a less drastic change in position of the accelerator, but that may be because you're not really expecting it to change drastically then. This is dangerous. If I need to get the hell out of the way of something coming at me, I don't want to wait a full second for the car to figure out that I've pushed the gas pedal. It does the same thing if I'm already driving and have to suddenly press the accelerator down to speed up. You can literally mash the pedal to the floor and then lift your foot back up with absolutely no change in engine speed on the car!
While the first issue may not be an electronics issue, as we're not really sure, the second, third, and fourth issues certainly are. In the hurry to make everything electronic, I think they've introduced some serious reliability issues into their vehicles, which is a shame because growing up I always thought of Toyotas as being of high quality and reliability. I still wouldn't hesitate to buy an older Toyota, in fact I've been looking at getting a late 80's 4runner, but I don't think I'd buy a new Toyota right now even if I could afford to.