The first difference is that only the second sentence is grammatical.
“I’ve done what should have been done” is grammatical, without a specific pronoun; here the prefect tense is a kind of passive, so that there is no subject for that part of the sentence — some action needed to be done by *someone*, and “I” did that action. If this is what you mean, it is okay.
The second difference is that the second sentence has a clear focus on the speaker’s own actions.