I don't dislike Rose at all; at the time, she was the viewers eyes into the Doctors world, and later helped differentiate between 'worthy' companions and other flotsam and jetsam.
Later, 11 would kind of echo this when he says he doesn't know why (he chooses people) he just knows who (he has to choose).
But, Rose did start the 'uber companion' trend, being Bad Wolf. Then Donna does it; then Rory/Amy, now Clara. Maybe even River.
Only Martha was relatively normal, and look where that got her, shunted to Torchwood before bailing out for CSI UK (or whatever it was).
So I agree that Rose deserves pride as place of the first companion of the new era.
And, I'm starting to think that Moff didn't really have any choice, because he has obviously gone through all the Time War references with a fine-tooth comb, and he could hardly ignore that 'I end the Time War' line from POTW.