I see where you're coming from, but I have to disagree. Popularity isn't everything. Sure, it is a majority of what gets MOST characters in, but it isn't the be all end all argument.
For Brawl, Megaman was the top 3rd party request aside from Sonic, and Nintendo didn't even ask for him. Whats not to say it won't happen again? Because Namco is helping with the game, I personally (yes this is my opinion) believe that to not expect a Namco character in a crossover fighting game is to set oneself up for disappointment. Obviously, this sort of agreement isn't solely to get a character in the game, but surely Namco wants someone in, and surely it would seem like a slap in the face to not include a character.
Think of it like this. Sakurai includes Snake as a favor for Kojima. So that is a little different. However, this is a partnership that Sakurai must surely appreciate. Namco getting a character should not be out of the realm of possibility, whether it turns out to be Pac-Man or Lloyd.
Surely partnerships don't necessarily mean that the company assisting with development gets something nice within the game. Camelot helped with Mario Tennis etc...yet they didn't get anything. Yet this argument doesn't really work with Smash Bros. Smash Bros. is a crossover fighting game, including characters from all sorts of different games and universes into one title. Surely, even if a Namco character doesn't get in, it will at least be considered.
You're right in that popularity isn't everything (and thankfully it's the case, else we already would have a few undeserving characters on the roster), but I do feel as it would really help with the case for a Namco Bandai rep. Unlike Snake, thanks to the announcement of Namco Bandai working with a character, there is an expectation among the majority of speculators of a Namco rep. Not to say that a third-party needs popularity to get in, but I do think that had fans almost universally agreed on a Namco rep and push for one instead of splitting into different fan base, a Namco rep would fare a lot better.
It makes sense why Mega Man didn't get into Brawl (aside from being third-party) because Sonic was by far the most wanted character (nobody else, Nintendo or third-party, came even close). By the time they decided to add Sonic, there wasn't enough room to add another third-party (or at least Sakurai saw no one else worthy of one). Plus Geno was a more popular request than Mega Man anyway, so it wasn't like Mega Man had much of a chance.
As for Namco wanting a character, we do know that they have interest in getting their characters in Smash, but I highly doubt that they will see not including one of their characters as a sign of disrespect. Third-parties are not a privilege, they are a special treat that should be used very sparingly (they don't have to even be used). If Sakurai were to add too many or select the wrong kinds, third-parties stop being fun to most people and people begin to hate it. Every third-party character inherently increase dissenters, so it is best to pick the ones that will please more people than upset. I think Namco will view a Namco character in Smash as something they would like to see happen, but given their third-party status, they will not feel entitled to having one. If one gets in, good for them, but if not, it won't fracture their relationship with Sakurai. Hino, president of Level-5, probably wants a third-party more than anyone, but you won't see his feelings hurt if Layton doesn't show up in Smash (and neither will any other third-party company).
The fact that Namco Bandai is working with Sakurai, legendary director of the Super Smash Bros. series, is rewarding enough because they have the opportunity to help co-develop the game and help work on the game. It'll be a great experience that they won't ever forget. Including a third-party character from Namco is simply an optional icing on the cake.
That said, a Namco character will probably be considered as you said. I just don't think that the final result will result in a Namco character.
Welp, no Kid Icarus characters other than Viridi, Magnus, or Dark Pit, then.
I was referring to characters in licensed games, not loosely based one. Should have clarified that stance.