Sure there are multi tiered structures of various types. Markets and Banks, libraries and Universities. But those AREN'T THE ONLY BUILDINGS, or even close to them!
The religions were completely interchangeable in civ 4, except for a few subtleties (tech age, resource bonus for cathedral). What they were meant for, was rather to give you additional goals and modifiers to other aspects of the game. If you wanted to persue a religion or try to found one for the economic bonus, that was an additional early game THING to do. If you wanted to get the most out of the religious civics, you'd have to use missionaries. You could try to spread it for diplomatic bonus'. These were all decisions to be made and weighed against each other.
Where are the interesting early game decisions in civ 5 to replace it?
Here's a good civ 4 example you even touched on. Happiness from a temple wsa the same as 1 military unit from the powerful early game civic Hereditary Rule. The temple would last forever, so you could build that now, but the military unit could be cheaper... and would be a military unit. Then again, it costs maintenance, so maybe it isn't worth it. Of course if you are in hereditary rule, you may plan on ways of efficiently turning population into the economy you'll need to support the larger military, or maybe you gun for military state to make it work better.
That's the kind of complex decision making involved in that game. Early rammifications, late game ones, questions of progression, questions of stability. I just haven't found the same to be sayable about civ 5.