I just went through this decision myself, and I opted for a '05 Focus wagon. I looked at all of the cars mentioned, and here's why I went for the Focus
-Matrix isn't as big; it's a hatchback, not a wagon. It's not really that close, 21/53 cu. ft vs 36/73 cu. ft seats up/down. (if I did go for the Matrix, I'd probably opt for the AT for reason you mentioned).
-Fit also has less cargo capacity, and the highway gearing with the MT is way too short for my tastes. I do a lot of highway driving and that's a deal breaker for me.
-Subaru Legacy or Forester. I don't want the extra complexity and fuel economy hit of AWD, and I'll be using this car in the snow. I've opted for FWD and snow tires.
Good things about the Focus wagon:
-depreciation! They're cheap. I got mine for 5K, '06 with 89K miles, 1 owner excellent condition, along with a set of almost new steelies w/snow tires.
-highway gearing is reasonable.
-from '03 on they seem quite reliable and pretty low-maintenance, and parts are plentiful and cheap.
-SPACE! At some point I'm going to swap the seats with some from an SVT, as the rear seat bottom isn't split (not a bit deal for most folks but I need the flat floor on one side). Right now I'm using it as a two-seater and I can fit 4 bikes, 2 dogs and a weekend of gear all inside the car, no problem:
-handles surprisingly well, engine and transmission are quite nice.
There are a couple of small maintenance issues (wheel bearing longetivy, hatch wiring and PCV hose cracking), but overall these cars seem solid. I opted for an '05 or later because I wanted the Duratec vs. the Zetec, but I wouldn't rule out a really good condition Zetec.
Two big potential issues: these seem prone to rust (not an issue in my hood) and the automatic transmissions seem pretty questionable. I saw a lot of these that looked in great condition with AT's, but I decided to bide my time. Finding one with a manual transmission may take some patience.
I'm on my 3rd tank of fuel, first tank was 31 mpg in mixed driving, next tank was 34.5 on about 80% highway in the mountains. No way an older small SUV will be close.
One other car worth considering if you really want a small SUV: A Saturn Vue 4 cylinder with a manual transmission. Again, hard to find but they're undervalued with a very solid drivetrain.