I should warn everyone that I retconned the shuttlecraft Copernicus, which we didn't see until the Enterprise-A, back onto the refit Enterprise. Because reasons. Discuss. I will take lashings with a carp as needed.
On a scale of "irreconcilable" to "not actually a problem", I'm pretty sure that "shuttlecraft names" are towards the right-hand end of that scale.
But I took the whole shuttlecraft, not just its name! None of the odd little shuttles glimpsed in Star Trek: The Motion Picture served my needs, so I just decided to give the Enterprise a proper big shuttle. I like to think it was sitting in some corner of the shuttlebay already, we just didn't see it in STTMP.
Actually TMP never really gave us a good look at the full-sized shuttlecraft glimpsed in the hangar-bay matte painting. But in Mere Anarchy: The Darkness Drops Again, I gave them their day in the sun and showcased their modular design as shown in this Andrew Probert sketch. However, in Ex Machina, I also featured the torpedo-shaped shuttle Matt Jefferies designed for Phase II as an extra-maneuverable atmospheric shuttle. So it's plausible the ship could've had other shuttle classes aboard.
I shall call this the Bennett Loophole and refer anyone disappointed in my choice of shuttlecraft to this post.
Here's the one: http://memory-beta.wikia.com/wiki/Zhang_Sui I remember that sketch from the Reeves-Stevens Phase II book.
According to Memory Beta, there's a shuttlecraft Copernicus of unspecified type assigned to the Enterprise in the 2270s. It could easily be the same one as in the novel, and/or the E-A one (with a new registry).
There was no review thread yet, but I have created one: http://www.trekbbs.com/showthread.php?t=248467