I enjoyed the new film a lot, but the 'alternate timeline' stuff was a bone thrown to us fans, and it probably hurt the film for casual viewers, I think. I say if they wanted a reboot, they should have come straight out and said it, rather than adding in all the time travel stuff.
My initial reaction was basically the same, that the Spock Prime stuff was responsible for the movie's most glaring problem (its hopelessly tortured plot), and that the writers would have been better served to go with a straight reboot minus the time travel and connection to the Prime universe.
Still, it's hard to compare something that exists with something that does not exist. The movie certainly seemed to be palatable enough for the masses despite the fanwankiness of the Old Spock element. Orci and Kurtzman seem to mainly excel at repackaging existing material, so perhaps their attempt at a straight reboot would have been a weaker story, not a stronger one.
At this point I don't think it matters too much, as long as the writers/producers are smart enough to let the new universe stand on its own for the sequels.