Everyone is offering the same reply so let me be devil's advocate here- how long ago is it since you got the substitution? You say the back was looking was looking wrong, but then say that it is the top you don't like the look of.
Just to be clear- I do think the shop was wrong, but I also think that you should have raised it as soon as you saw the first substitution. Your message says that you did raise it a few times and that is what I would be focussing on- "I mentioned to you on X date that I did not think it was coming together like the sample and that is when you should have offered to make good. Instead I have invested more time and money to get something I did not want".
Otherwise, with the attitude they have displayed so far, I would expect the shop to just say, "well, you have had that fabric for months now and you never noticed it, so weren't our subsitutions great" Not saying that is right, but that is probably what they will do.......
Caveat Emptor- let the buyer beware- sad, but true. :-(
Sorry you are not happy with your quilt- do raise it them with and put it to them specifically what you want them to do to make it better. There is no point making vague complaints, in my experience- state what happened, tell them what you want. If that doesn't work, tell everyone, and/or stop buiying kits- I had no idea this was so widespread but I bet it is in the small print and they will probably have covered themselves legally.
Sounds like they are a busy shop. Are you in contact with others who got the substitution? You say it was half- if they are not happy either the impact of several people raising it with them (with the same request) will be much harder for them to ignore. Otherwise they will come back with the old favourite "most people were happy with it" and try to make you the one who is wrong. Not nice, but a lesson learned. It obviously happens a lot.
Good luck with it. I bet you'll salvage it to look good in your new room.