Yeah, I know, I know... But being able to do what Sakurai forgot to do with those two, changing even one attribute, would help me accept them a bit better.
Consider Lucina and Dark Pit as glorified alt costumes.
They were meant to be alts, but the very slight changes (which by the way Sakurai talks about Lucina seem to be somehow accidental) were the reason they were given their own slot, as to not mess with the game records.
Given the statistical nature of game records, no matter how minimal changes may be between two different characters, they would be skewed if two different characters shared the same slot. If the records are meant to be exact, no detail, no matter how small, should interfere with a precise tracking of character usage.
My theory is that the development team was tweaking around with Marth and Pit and came up with those now alternate versions and decided to keep them by splitting Lucina and Dark Pit, upgrading their alt status to a standalone character. It's not that outlandish, considering things during development are never set in stone until the project is declared finished. Tweaks and slight changes happen all the time during development: I know it from programming experience.
It also likely helped Lucina and Dark Pit have a significant amount of popularity, mainly in Japan, to the point there's merchandise of them there. This makes their inclusion a bit more justified. They're very much this:
http://tvtropes.org/pmwiki/pmwiki.php/Main/EnsembleDarkhorse
The fact they're very similar may also have to do with balancing, given they were made late in development.