Okay, maybe it doesn't strain credibility too much to have Kirk and Spock meet as teenagers before either joins Starfleet; canon doesn't give us any detail on how long they've known each other or when they first met. And canon doesn't say much about Kirk's brother, so maybe he was a drug addict involved in an alien crime ring before he ended up on Deneva with Aurelan and the kids.
But the idea that Kirk is a genius engineer and hacker, estranged from his father, just doesn't quite feel right to me. The idea that, even before joining Starfleet, he manages to steal the Enterprise from Spacedock and fight the bad guys and blow open an Orion conspiracy... well, that's where we go from "I'm not sure I buy that" to "this is utterly preposterous." James T. Kirk is not just some guy, sure, but making him so much of an overachiever so early takes away from the Hornblowerish self-questioning and self-doubt we see in some TOS episodes.
The portrayal of Spock as a somewhat insecure teenager still not fully in control of his emotions is solid and believable. He's handled pretty well in the story, but I'm not sure the Vulcan artefact smuggling that he stumbles across is really thought through. The bad guys are knowingly buying supposedly stolen forged Vulcan artefacts with tech that fools sensors into showing them as authentic in order to get the tect to use it for another purpose. But how did the process start? Did the bad guys think, hey, let's try to steal Vulcan artefacts, so they'll create fakes with the kind of tech we need? Did the Vulcans think, it is logical to assume that our artefacts may be stolen, and therefore they should all be replaced with forgeries equipped with technology that will enable them to deceive the thieves and their sensors? Maybe that was addressed somewhere and I missed it, but it felt like Braga/Menosky TNG/Voyager plotting: come up with a mystery, add a twist to the mystery, add a surprising explanation to the mystery, but don't look at it chronologically to see if it would actually make sense.
I did like the way the story dealt with the backstory from "The Conscience of the King." It explains why a farm kid from Iowa was on Tarsus IV, it explains why only a small number of survivors could identify Kodos (instead of everyone who wasn't killed during the incident), and it gives the young Jim Kirk some somewhat surprising but plausible characterization.