Lucina's popular and important enough to be her own character, the Trainer's aren't separately. Another thing is that Lucina can be unique if you really wanted to make her unique, but regardless I see no real flaw with her joining the Smash Brothers roster. Only reason I think people write her out is because she disguised herself as Marth. But there was nothing that really made her seem like Marth other than her hairstyle when disguised and the Falchion. Otherwise we'd be calling her a completely different character and we'd probably advocate for her along the likes of Chrom and Robin. She's literally just as important as them in Awakening anyways.I really don't care what they are called. However you look at it, it's the same gameplay concept as making Male Wii Fit Trainer a different character. It's taking a character with the same basic model and design who's only difference in appearances in gender and making it a separate character. Maybe I used bad terminology. But, making either characters separate as their own slot is just as bad.
I can't really think of ways to make two Wii Fit Trainers work (there may be enough of other fitness styles for the Male Trainer to adopt though), but I can think of ways to make Marth and Lucina co-exist. It's not as bad as you make, it's not like Lucina is a worthless unimportant Fire Emblem character. But that's just me, you can think what you want.