I see a lot of "just accept the gift" here, but that's a rough choice. If you accept the gift, then you would be expected to use it over the one that you like. Your wife may even go so far as to throw the other one away (depending on what it is). So I don't think accepting the gift was ever an option.
It really is a hard spot to be put in, and I would have probably done the same thing in your position, even though I hate denying gifts. The whole premise of gifting is flawed, imo, at least where I'm from. To me, the one being gifted is put more on the spot than the one gifting. I hate getting gifts for this reason.
So maybe this. Explain why you like the one you use better, but that you're very happy with the gift. Ask her if it's okay if you keep that gift as a backup if your first one breaks and store it by the first one "just in case". Its never bad to have two of something.