There's no way to tell what the fate of 3rd parties will be. There's simply not enough evidence to suggest much of anything.
Snake was cut in the transition between Brawl and Wii U/3DS, but there are outside factors.
Sonic was brought back. Granted, he's Sonic the Hedgehog, but he was brought back. This at least implies that both parties were willing to come back to the table. There's no reason to think Capcom would be against Mega Man (and by extension Ryu) coming back, nor Namco against Pac-Man returning.
Based on the interviews (granted, it could just be PR) Nomura was quite excited at the prospect of Cloud in Smash Bros. This game really does have clout among the gaming industry. A lot of different developers would only dream of having their own characters in Smash. Despite Final Fantasy being an extremely successful series (and Final Fantasy VII being the most famous/beloved/iconic) I don't think it's hard to believe that Nintendo would come back to the table.
I mean, it's freaking Cloud. He's not just an "anime swordsman" like a lot of people here would like to think. Cloud means something to the industry.
I would agree with the licensing argument, in that Nintendo needs to save money, if I was convinced that retaining each of the acquired 3rd parties would mean a potential negative for the bottom line of the profit margin, I might agree that it would be an issue...but as of now I'm not entirely convinced. For all we know, Sakurai/Nintendo might intend to go back to the negotiating table for any 3rd party they acquire (except for Snake).
One last side note...If you're Nintendo/Sakurai, and you view the acquisition of Cloud as a "miracle", why wouldn't you at least try to acquire the character again, especially if the company that owns him was willing to work with you the first time?
This isn't directed at anybody in particular, but if it worked the first time then there's no reason to believe it couldn't work the next.