I'd say prime examples of what a "semi-clone" should be like would be Doc; the right kind of changes to make it so they feel different in playstyle, but don't require heavy man-hours to create. (I don't really consider Wolf a clone, nor Falco at this point; Lucas I would honestly say was at Luigified status from the beginning, having a few similar properties but a lot of other different things.)
Competitively, Lucina is sadly outshined due to her design. I'm guessing she's primarily placed at Underwhelming because there's little reason to use Lucina (a bit similar to why Doc is better than Mario in Melee, or at least my opinion; at the highest level of play, Doc has that slightly better matchup with spacies, which is why he's higher) because Marth will get you better results and simply has better abilities. I personally don't see Lucina as bottom 10, but she's definitely a step down from Marth to the point where she will be at least a few spots down.
There's a reason why there's the "A skilled Roy can beat any Fox" joke. Melee Roy is completely invalidated by Marth and he's bottom 5, 3 or even sometimes considered the absolute worst character in Melee. (But this thread isn't about Melee, yeah? It's about Smash 4) because of the fact that his changes just make him even worse, giving him less effective tools. Fortunately for Lucina, she at least has a carbon copy of Marth's moveset, save for physical attributes and her blade.
Dark Pit I think should still be placed right next to Pit and I agree with the stick to it. Yes, there's changes and the arrows and the Ftilt are notable, but they are literally carbon copies of each other with slightly different tools for each occasion. A minor advantage shouldn't really put Dark Pit a few spots behind Pit unless it's a major issue of turning one matchup from an advantage to even or disadvantage.