Codyoliver:
Bob's right...pretty rare that we can't make things work out MOST of the time.
There has been an instance or two where I had to replace the leaded pipe/flange and the darn thing just would not line up with the old toilet hole. See, when they used cast iron and were installing lead pipes, most of the time they ran things square and no issues...OCCASSIONALLY, one of these guys just shot the drain line out at any *willy-nilly* angle they wanted too...hard to match up to that when fittings of today are rigid and fixed and follow specific angles.
Now, with that said, I think Bob's right, an offset flange could probably have helped here......or plumber could have used a 22.5 degree fitting to offset the pipe over (if room). Call the plumber back and ask him if these were options he tried...or that he COULD TRY NOW

...see what he says.
IF he will not fix..or can prove somehow that he cannot improve the fit, then they do make toilets that are roughed in for 14 " (most are 12" like Bob said). THIS stinks, of course, but would give back the finished look you had before (just an option for you).
Measure from the finished wall behind toilet (not off baseboard -->>off the finished wall) to the center of the toilet bowl caps. Tell us what that measures. Also, tell us what floor this is on..ok? Talk soon...MARK
.