Okay, I'm going to make this abundantly clear: Even if one were to apply custom moves, Olimar would still be the worst character in the game--especially since they don't help him or his problems at all one bit. Why? Well, the big reason is thus: Because the Pikmin move at only 30 FPS, that means their effectiveness is doomed right from the get go. The customs cannot possibly help, and the improvements that they do make are minimal at best. People are giving Palutena crap, but at least her custom moves help her; at least she has a usable defensive gameplan. Olimar cannot cover up his weaknesses at all.
Now, as for my controversial move to keep the clones in separate tiers from their original counterparts, the minimal changes are a very big deal especially when it comes to tactical uses. For example, Lucina is nimbler, but lacks a tipper; Marth possesses one. Dark Pit, meanwhile, cannot change the trajectory of his neutrals as well as Pit can, but his side special has electric properties, whereas Pit does not (Dark Pit is also slower, yet stronger than Pit). And lastly, do I need to mention the many differences between Mario and Dr. Mario? It's these little things that ultimately changes the way each of these clones would have to be played, even with the implementation of custom moves.
Let me use Lucina as a big example. Because Lucina lacks a tipper in her attacks (and since the hitboxes for both of these characters are not as good as they were in past games), it means she cannot zone and control the space as effectively as Marth can. As a result, the best course of action with her is to adopt a more defensive gameplan; wait for the opponent to make the mistakes, and then let them have it. Custom moves benefits Lucina better than Marth does, with the exception of the third neutral, however.
Dark Pit is a bit of a different animal from Pit, but Pit is designed to be more of a tactical fighter and thus will get more leeway off of custom moves than Dark Pit (though not as much leeway as, say, Lucina would in comparison to her counterpart); Dark Pit, meanwhile, feels more like a beatdown type of character, which doesn't exactly help this sort of character. At least Lucina's placement is disputable compared to Marth's, but Pit just screams better fit for a more fitting plyastyle (you can't exactly play tactics very well with Dark Pit).
I could go on and on with Mario and Dr. Mario, but I think the general consensus has it that Mario is simply much better this time around.
And while I have yet to unlock all of everyone's custom moves, keep in mind that Marth and Lucina share all of the same moves; and Pit and Dark Pit have the same specials save for the sides (and even there, it's consisting mainly of different properties). And I already have all of Lucina's and all of Pit's.