After they made such a big deal about Mewtwo in Smash 4 (being the first DLC character, a reward for people who purchased both versions, the subject of a weird tease in the 50 facts video and a clear response to the fan demand for his return) it only made sense for Mewtwo to stay for good.
I think Sakurai is done with mass decloning in Smash by now. He knows that people like playing characters as they are, and Smash Ultimate really didn't feature many moveset revamps for that reason. I think Echoes will stay as echoes, otherwise the numbering thing gets really weird.
We can change the echo title to something else like an alpha echo. And all alpha echoes are based on the character but are unique now.
So we still have echoes like Daisy but others would be alpha echoes. Or just still call them echoes still because he feels like it and that's why Ken is one and Chrom has a move from Ike.