First, we need to stop putting Isabelle into semi-clone status. Aside from aesthetics, she shares very little in common with Villager. Same dash attack, same neutralB, similar upB. Are Lucario and Mewtwo semi-clones too?
Second, even though Snake, Y. Link, Pichu, Wolf and Ice Climbers aren't newcomers because we've seen them before, they needed to be recreated from the ground up in the Smash Ultimate engine, with brand new textures, 3D models, animations, etc. Nothing can just be ported from Melee/Brawl. They have direct references to use, so the characters kind of skip the concept phase, but past that, they take substantially more work than echoes and more closely resemble newcomers in terms of work load.