On the topic of Ace Attorney, obviously franchises with more notoriety are gonna be the first choices. That's a natural decision that just about any company would make if they thought they could get the rights at a decent price.
That being said, it's not like Nintendo's been following a clear pattern with these characters. After Sonic, we got Bayo and Joker. Neither of these characters make sense as the second and third Sega choices if we go by sales, iconicness, or fan demand, and yet here they are. Similarly, Nintendo's previous third-party choices didn't help Sephiroth's case, and yet here we are. Nintendo opted for a second FF7 character before a new franchise.
Point is, there's no telling what logic Nintendo will go by at any given time. Sometimes they opt for the big name, sometimes they throw us a bone and give us the fan favorite, and other times they choose something seemingly random. Just because a franchise is "next down the ladder" or a character is more iconic than another doesn't necessarily mean they can't be overlooked for someone or something smaller.