Hi!
You're really asking too many vague questions but I get the feeling you don't know what to worry about and what to ignore for a first design.
All your questions sound valid, and in engineering you need to figure out what can be ignored, but we need specific information!
The speed of propagation of a signal on a PCB that fits on a desk is not much of a concern at 1MHz, for example. But I'm sure you can always find an exception. I can think of a few.
Here's the deal, for I2C you need to worry about capacitance, that is how many loads you slap on to the bus. Even though a signal by itself could get to the destination fine by itself, if you start putting many loads you slow down the edges of the signals and that's what can cause problems.
So we need to know what speed of I2C do you plan on using? How many thingies are you slapping on there? How big is this board? "small form-factor" may mean something to you, but it means nothing to me. What size? We need numbers!
I don't know what you mean by this question "is running a signal trace above the same signal trace (top layer, bottom layer) bad practice? ".
What signal? What layers? What PCB? What connectors? What signal A and B? What shorter, but how much? A mile? A quark?
This is the only way you can expect useful advice.