Point by point:

• Define “thriving”, since it's the main objective of the whole game. What are the differences between the “ages” going to be?
• What does the terrain do? If you planning something more complex than the random tiles and structures in, say, Master of Magic or Civilization, is it really valuable?
• Shouldn't the simulated citizens take care of themselves and of the city without “hiring” special characters?
• What gameplay changes come with upgrades and new buildings? For example, what's the difference between a bronze age temple with an altar in a straw hut and a modern large cathedral?
• Moving elsewhere (as opposed to expanding or founding colonies) should probably be considered a miserable failure (the original city doesn't thrive)
• Settlers don't remain settlers for long, and they are normally competitive, not “evil”.
• What in-game characters (certainly not the whole city) are going to engage with dungeons and minigames?
• Are “dungeons” appropriate for every era? Including an ultra-high-tech endgame?
• What do you mean by "tile matching" and “merge” in the context of city building? Are there other forms of war than tower defense?

BradleyAuerbach said:
Game Concept A survival/idle city-building game where you have to help a group survive while building a base that progresses from the prehistoric era to the future.

Perfectly fine concept. Go make it. Or write the design concept, then put it aside and get another. But the concept is good.