The more promient franchises should get in?
I don't think that really matters at all. I mean just look at Snake, he's had 1 bad port, 1 spin off, and 1 remake on a Nintendo console. Compare that to Simon Belmont or other Konami characters, and I don't think proment matters at all.
Snake got in at Kojima's suggestion and Sonic due to fan demand. I don't think there is any real method for a 3rd party character just yet.
Generally speaking, yes. The more promenent franchises should, and if it's up to strictly fan demand, will get in.
Megaman is the loudest voice right now. We all agree he has the best shot. Dragon Quest may have connections with Nintendo, but Slime's inclusion will be mixed in terms of worldwide reviews, and demand will be as well. Most of the world hasn't opened up to the franchise the way they have to Mario, LoZ, Megaman, and Final Fantasy.
Final Fantasy and Megaman, are more bang for your buck, and that's just that.
Snakes reasoning is something we won't see again. Friendships favors. We could see mutual parties coming into agreence to add a character, or fan demand pressuring Sakurai to make the first move, but I am betting you we will not see another Snake incedent. Unless Kojima wants to bring Simon or the White Bomber in, I don't see another Snake incedent happening again. So he is pretty much a poor example. Sonic is a better example of what to expect. BIG NAMED CHARACTERS who show a prominence in Nintendo history.
Dragon Quest and Street Fighter have a slight hitch though. Nintendo has taken a liking to DQ, and whoever has been in charge of SFIV and SFxT is showing a lot of interest in 3DS installments. Star has theorized that if we got a SFxT on the 3DS we may see a Mario or Marth or something show up on similar to how the PSVita got that lame guy no one cares about. You can see the scratching of backs happening there.
OTHER THAN THAT, it's going to come down to fan demand, and big names always win out there.
Also, INafune's King of Pirates looks fantastic. The first thing he's ever made that truely sparks my interest.