Can I use these both interchangeably?
You are a lot taller than I thought you would be.
You are a lot taller than I thought you were going to be.

Question

Answer

Yes you can. They're both correct.

Answer

Well 
Should I use a lot taller or much taller ?

Answer

These are both fine to use but the first sounds more natural. 
For the second one you could say it casually:
"You're a lot taller than I thought you were gonna be".

Answer

The first one sounds much more natural.