I'm trying to make the same decision. I haven't driven either of them yet, but each one has their pros and cons on paper.
The Matrix is only 3 inches taller than the P5, so there isn't that much difference in height.
What I've found...
Pros for the Matrix base/XR - Toyota reliability, gas mileage, slight edge in cargo space, higher resale value
Cons - higher ride height, crap torsion beam rear suspension, may be a little more money with equal options, but the base can be had cheaper
Pros for the P5 - sportier, more fun to drive, 0% financing or lower resale value (if you're buying used, that is a pro)
Cons - Reliability record not as good as Toyota, weak engine (but it is ULEV), rated gas mileage is 5mpg less (and that adds up when driving over 25,000miles/year)
As far as straightline performance, I think the nod goes to the Matrix Base/XR (XRS is much faster, but more expensive and that engine doesn't belong in the Matrix. It fits the Celica's personality much better). Aside from mags times showing the Matrix XR is a little faster, the real power and weight numbers would indicate the same thing. They both weigh about the same. They both have the same rated HP, and the P5's torque is listed as being higher, but in every dyno chart I've seen, Toyota's 1.8l equals or betters Mazda's 2.0l from 2000 RPM to redline. And the Toyota has a little more up top. Typical 1ZZ dynos show 110-120HP to the wheel, the P5 dyno on flyinmiata.com website didn't even reach 100WHP.
Of course, the best way to decide is to drive them. And as soon as the roads aren't covered in salt and s***, I'll do that.