I like how you have to be sincere to get the benefits of the virtue system. That way, the virtues shown are the cause and not simply the effect of ulterior ambition.
The premise is good and the system is supportive and reasonable. It's too bad that the main character is just a pervert with nothing much to say about. If not for the system, it's unlikely he'd have made anything of himself.
It's annoying because the novel is genuinely interesting and introduces a lot fascinating historical tidbits. If not for the random biases, prejudices, and propaganda pinging like random rock metal notes in a classic symphony, it would be far far more enjoyable. How in the world an archaeology graduate throw the sins of the British Empire to those Mithra believers? They're not even the same people, and separated by more than a millenia. In general, all his novels tend to have that distinct Chinese superiority complex idiosyncratic to the setting.
How to say this... I know it's fiction but even though he has a broken godhood, he's far from being able to rewrite natural law. In short, if he doesn't expose the soil after tilling it, parasites, fungi, and the sort should affect the plant. He replant the first crops and the next without fertilising them. Even if he uses magic to speed up the growth, it should consume nutrients (that's not being replenished) and shouldn't be able to grow that well.