There's not difference on meaning.
For example:"I like brown bag"
나는 갈색 가방을 좋아한다 : emphasis on "(like) brown bag"
내가 갈색 가방을 좋아한다 : emphasis on "I"
Both are same meaning.
More example.
"I ate candy"
저는 사탕을 먹었어요. : focus on "candy"
제가 사탕을 먹었어요. : focus on "I"
(Both used the honorific)
"Who ate my candy?"
누가 내 사탕 먹었어? (non-honorific)
"I ate it."
(honorific)
제가 먹었어요. : Correct
제가 사탕을 먹었어요 : Correct
저는 먹었어요 : Strange
저는 사탕을 먹었어요 : Still strange
Because he wanna know "WHO ate that", not "candy".
but
"I didn't eat that but John ate it."
저는 안 먹었는데 John은 먹었어요 : Correct
저는 안 먹었는데 John이 먹었어요 : Correct, more focus on snitching than before
제가 안 먹었는데 John은 먹었어요 : Correct, and more focus on "I'm better than John"
제가 안 먹었는데 John이 먹었어요 : Correct