Learn English – How many stations “is it?” vs “are there?”

Let's try some minimal pairs:

• I walk rather than run

• I walk instead of running

• I eat apples rather than oranges

• I eat apples instead of oranges

• I walk quickly instead of quietly

• I walk quickly rather than quietly

I don't really think there's much of a difference, except perhaps rather than implies preference whereas instead of implies substitution. But that might be nitpicking. And it doesn't seem to apply when using it to coordinate adverbs (last pair).

Also, there's a slight difference in the verb forms in the first pair, but there's not really a difference in meaning there.

It's a small but important usage distinction.

I never thought he would stoop to such levels.

This is used to agree that the person being discussed has failed at some point of character and the speaker is shocked by the fact. Equivalent: "I didn't realize he was such a bad man."

I have never thought he would stoop to such levels.

This would be used more often to suggest the opposite, to reassure someone that the person under discussion probably had not failed a particular test of character. It's the equivalent of saying "I've always thought he was a good man who would not do such things."