In the case of Pit and Dark Pit, it's actually fairly easy to make a clone like Fox and Falco.
They are similar in appearance. But that's easily fixable.
Those are Pit's recolors in Brawl.
For Dark Pit's recolors, give him
silver/gray instead of
gold,
blood red instead of
pink,
lime instead of
forest green, and
dark blue or
indigo instead of
light blue.
Also, it's easy to keep the color of his wings black with a hint of another color and make all of Pit's wings white with a hint of another color. Along with that, concept art shows that Dark Pit's wings are actually slightly different:
They're slimmer and that could be implemented in Smash.
Then, give him different kinds of weapons than Pit.
^This^ is Pit's arsenal.
These are the weapons that Dark Pit has canonically used.
Of those, these can be used to replace Pit's moves:
And we can change his down special entirely or have him use a power like Reflect Barrier, Bumblebee, Brief Invincibility, Energy Charge, Libra Sponge, or more that could all have similar effects and be cloned from Pit's down b.
Dark Pit also has the power to fly after he absorbs the power of Pandora. Because of this, it's entirely plausible that Dark Pit could use Pit's old Up B and glide. And be a more aerial-based clone of Pit, since Pit's now much more ground based.
That also gives a reason for including him. In Uprising, you go between land battles and air battles. Right now, Pit seems to represent the land battles far more. Dark Pit can be the opposite.