Wow, you raise some very good questions, Lord Reliant!
1) I would say that resources such as metals, diamonds, gold, etc. probably would still exist within the mountains and hills. And you are just bringing back the "green" to be able to grow crops again? So this might raise the ability and or strategy that you could have mining villages in lands that are still infertile and have food shipped in? I think this would be cool, but idk this is a hard question
2) I would imagine that heroes are going to be leaders of small villages that are scattered across the countryside and when you stumble upon them you can ask them to join you and whether their villages join you along with their leader would be another thing entirely. I would suppose imbuing their land with life essence would go a long way in convincing them tho I think it would be cool if heroes had their own beliefs and would join a certain nation more likely than say, yours, if your beliefs did not match and so it would take more convicing from you to turn them over to your beliefs and thus to your side. So while you may give their people the ability to grow a lot of food again and allow them to grow and prosper, they may never join you and might just use your kindness against you one day!
3) Yes.. this has always frustrated me about games like these. With Civilization, I actually never really noticed it all that much as the turns went up by like 50 years sometimes and the more important population reference was the relatively small number next to the city name anyways. But with GalCiv, as population was an important thing for taxation, i always wondered how those millions of babies being born each week (or turn) were paying taxes as soon as they were born <(goo goo) <(umm... you gonna pay this, kid?) I mean come one! lol But yea, I mean that was when a turn was a week! Now they are in days!?! Yea, I have no clue where I am gonna find my army now, I mean babies might be able to pay taxes but they certainly can't fight! It will be interesting to see how this is handled because I have definitely drawn a blank here...