No answers (don't want to let my Prius snobbery show y'know

), but some more questions that you didn't mention -
:: you don't want to put the seat down to transport the PDs if you don't have to. Why not? Do you usually have more than two people in the car? The back seat on my Prius (and on the two Subarus I owned before it) basically stays down permanently. Can your dogs stand comfortably in the Prius? If they're crated in the car, do their crates fit equally well in both cars?
:: you say the MPG advantage of the Prius "disappears" when you put bikes on top, but if you get 30 mpg out of the Prius with bikes on top, that's still got to be better than you get in the Matrix with bikes on top. Last I put bikes on top of a small car was quite a while ago, but it would normally take 25-30% out of the gas mileage on my '87 Duster.
:: gas prices aren't going anywhere but up. They're not making any more of it.
:: If the Matrix is a 49 state car, then there's emissions to consider as well, since the Prius is a 50 stater.
:: what do you tow, and how often? Is it worth keeping a car just for its towing capacity, or might you rent a truck when you need one?
I wouldn't be concerned about "unknown battery issues." It's just a NiMH battery, that's old tech, and it's got a 10 year warranty on it. Worst case, if the hybrid battery should die, you're not stranded, because you've still got the gas engine.