I have the Houdini and the Ion, both of which are pretty nice. I haven't used them a great deal yet, but I'd say the Houdini is a bit more water resistant, and the Ion is at least a little bit more breathable. The Houdini seems to be higher quality and more durable. I noticed some the Ion's stitching coming loose soon after I got it.
The biggest difference is the fit. The size large Ion is slim fitting, and the body is a bit shorter than a typical large sized t-shirt. The Houdini, also large, is very loose fitting on me (which is typical of Patagonia jackets), is a few inches longer in the torso, and probably about an inch longer in the sleeves. The Houdini's hood is large and has a slightly stiffened brim, whereas the Ion's hood fits more like the hood on a sweatshirt (snug, with no brim). The Houdini has a drawcord in the hem; the Ion doesn't. Overall, the Houdini fits like a very light rain shell, and the Ion feels more like a hooded, long sleeve shirt made out of wind-resistant material.
Depending on how you intend to be using the windshirt, you might want to consider sizing down with the Houdini, or up the with Ion.