When car was less than year old I noticed that sometimes it takes a little longer for it to start. I took it to a dealer and they said it's within specifications. I wouldn't call it a problem, more of an annoyance, but it's still there, so I've learned to deal with it.
Windshield wipers didn't turn on few times when I pulled the lever down, seems like something is wrong with the wiring around steering column, but it hasn't happened again in at least a year, so I'm not too worried about it.
Tires are wearing out quickly and need to be replaced shortly at only 35,000 miles. Toyota uses cheap tires that don't last long, and replacement tires are relatively expensive (at least in my book).
There is a strange sound coming from the engine bay, a friend of mine says that I have a lifter in one of the cylinders that needs to be adjusted. It can only be heard when hood is open, so it's not a major concern and most people would never noticed it.
Seats were covered with attractive looking cloth, but it's starting to show signs of wear. Camrys and Corollas of comparable year seem to have more durable cloth.
This is a car that can be called Jack of All Trades. It can haul a lot of cargo, it's reasonably comfortable for 4 people, it's easy to parallel park (although turning circle is a bit wide), it's fairly easy to service (I do all changes on my driveway without having to raise the car), it gets 30 mpg on average, and in over four years it never broke down. However there are a few little things that I feel every potential buyer should know:
1. Air conditioning is weak, you might want to think twice about buying this car if you live in Houston or Phoenix.
2. Although on paper 1.8 liter 130hp (really about 125hp) looks good, it's pretty slow due to Matrix being relatively heavy. If merging on a busy highway is a concern for you, maybe something more powerful will suit you better. Or you'll learn to use "Overdrive Off" button frequently.
3. Transmission is very smooth and accurate, but during hard acceleration it pauses for a split second, it used to kinda bother me, but I got used to it.
4. Dashboard design and layout is top notch and you'll get positive comments on it (get used to it), however driving on a sunny day with sunglasses on can be a little tricky.
5. Seats are cheap and uncomfortable (at least for me). I'm used to hard, firm seats that are supportive on a long road trip. Matrix seats are made with foam that feels fine around town, but on a highway driving I feel like I'm sitting on the pillow.
6. I'm 5'8" and I'm wishing it had more leg room, if you are 6" or taller you would be uncomfortable.
But all of the above could be counter-balanced versatility of Matrix, and if you are living outside of urban core, north of Mason-Dixon line, and you are a slim, short person looking for an efficient, reliable transportation from point A to point B this is a car for you.
I bought a 2007 and I find the leg room excellent I am 6'1"
but in order to do this you have to adjust the seat severall times
1. Toyota changed Driver Seat in Matrix around 2005, my parents have Base Matrix and it has adjustable Driver Seat, still my mom's Matrix is not much better then mine when it comes to leg room.
2. Maybe seats in XR/XRS have more flexibility, base model seat was a little Spartan back in 2002.