Advisers and other in-game help and pop-ups have always been more or less useless in Civ games. Turn off the ones you can and ignore the rest, and half your complaints vanish.
The rest are pretty nit-picky. If you look at the big picture of game development, a new release in a franchise is rarely earth shattering. Generally there are a few new features and systems, while the core game remains the same. That's exactly what we got with Civ 5.
I think if you played Civ 4 (I'm pretty sure you didn't) you would have a better perspective on where the studio put their resources. You can't have everything in a game; you have to choose where to innovate. From Civ 4 to 5 there were some huge changes, particularly the hex tiles and revamped combat system. That alone has improved my enjoyment of the game a lot. I used to find warring tedious, but it now seems more strategic and fun, with actual ranged attacks and such.
But that's just the tip of the iceberg. They revamped and improved a ton of stuff from the last version. You have to take the bad with the good, and hope that the balance is for the better. I think things like your Settler not carrying religion or not being able to remove mountains are pretty minor compared to the completely overhauled systems for trade, economy, combat, religion, etc.
So terraforming didn't make it in this version. Civ isn't a reality simulator, and game studios have limited resources. Maybe in the next version they'll decide to commit more resources to altering the map. But then there will be something else to complain about....