Toyota played the role of gracious host to Pontiac in the Matrix/Vibe development program. If the Japanese automaker had wanted to, it could have withheld some of the choicer components from Pontiac, especially since the two vehicles are built at different factories. But Toyota didn't, instead inviting Pontiac to partake fully of the Matrix/Corolla parts bin. That the 180-horsepower Matrix XRS is offered with both the six-speed manual and a four-speed automatic transmission, while the equivalent Vibe GT comes only with the six-speed, is because Pontiac said, "No, thanks, maybe later," to the autobox, reasoning that it didn't fit the GT's sportier profile.
Thus, the remaining differences between the Matrix and the Vibe are only in styling, perception, and cost. Beauty is subjective, and the Matrix hasn't been priced yet.