We've done all three, the CT x 3, QV x1 and the MDR x 3 (I think those totals are right, I'm suffering from pregnancy brain currently).
First off, you very well might be able to nab a table in the QVR. Even though there are only 4 tables, I've heard there are usually tables available. It can't hurt to try.
My thoughts.... we love V&A and try to go when we can. If price and all other things considered are equal (appetite, desire to try new things, etc), we would do the CT each time, followed closely by QVR and then the MDR as a nice backup. We really have become foodies and the little touches that you get in the specialized areas are worth it to us. We went to the QVR shortly after it opened and experienced some amazing touches that just couldn't be done in the MDR due to the amount of guests and space. I find the add ons in the MDR a pain in the rear, although they also exist to some extent in the QVR. I don't know if they are at the CT as well now.
I've walked away from every meal at V&A stuffed to the gills. DH and I always have our own wine pairings, we never split. And I can leave food on a plate, but never wine in a glass! (That's just wrong!).
Wherever you go at V&A, as long as you go with an appetite and some semblance of an open mind, you will have a great time. I say and open mind because sometimes Chef Hunnel even surprises the foodies (serving a Japanese inspired course with a wine pairing of sake, took me by surprise and I hate most sake- guess what? amazing course and sake).