The problem is that it mostly feels like I'm shuffling numbers around. I'm having a hard time getting immersed and feeling like the research and buildings are real things and not just stat boosts and unlocks.
I think I understand your problem. Civilization is kind of a game that encourages you to create objectives for yourself before setting up the game and than making an effort to reach those objectives. You actually can pick random civilization for starters and see where flow of time gets you, but much more fun is to have a plan beforehand. For example you decide that Elizabeth has to rule the world, and she has to be warmonger and in police state. Then set up your game and "make it so" (read this in Picard's voice).
Also you might want to adjust your timer for timer to flow faster (you can do it while setting up your game).
Don't know about how much immersion you can get, but civs can get pretty intense for me, especially if things go not exactly my way all the time.