So, you can get better seats besides middles pretty easily. In fact, I recently scored seat 62A-- a window with extra leg room-- on the 744 and had a fantastic flight in Y, on a Continental ticket. I certainly could have picked one of many, many aisle seats had I wanted one of them.

So you're down to two problems: no clubroom for Y flyers and no elite line. Two problems aren't "many."

In addition, if you mention CO, they might let things slide. I had an overly-heavy carry-on that they were going to force me to check, but I said I was flying on a CO ticket and was connecting from a CO flight, and that CO let me carry the bag on. They let me carry it on.

You make a very weak case for your "problems." Personally, I love the codeshare and think its one of their best.