Sakurai confirmed in Famitsu that ROBIN is the reason Chrom is not in.
Essentially, Chrom was planned, but Sakurai felt he'd be too samey, so he opted for Robin, who was more unique.
Lucina was intended to be a costume for Marth, but Sakurai decided to arbitrarily tweak her, so she became a character. She is samey, but she's basically just a costume with a slot on the screen. She's literally a BONUS character on top of the planned roster. She's not stealing anyone's spot. She was added IN ADDITION to the ALREADY PLANNED roster. Almost like a DLC that was already added in. On top of that, she was ALREADY in the game as a costume.
And there is no finite amount of slots. They add or subtract as they go along. It's not like they go LET'S PICK 50 GUYS and then someone doesn't make it because of 'slots'. They don't make it in because they don't. Nothing else to it.
Toon Link isn't blocking Ghirahim, Tingle, Impa, Skull Kid, Midna or Vaati from getting in because of a made up alotted amount a series gets. If Sakurai wants 6+ Zelda characters, he'll add them in. It's not determined by some slot number. Melee was only going to have 19-20 characters. We got more because of clones. Without them, we'd just have less characters, not different characters.
The bottom line is that Lucina didn't get in over Chrom. Robin did. So the roster would've been Robin alone or as it is now, with Robin & Lucina.
So if the roster was, say, 50 characters with Lucina, removing Lucina would just give use 49, with Lucina as a costume. We wouldn't get a replacement. She's an extra. OR we'd have just gained a different clone, putting us in the same situation..