"Deserving" is a wholly subjective term. I don't think anybody "deserves" to be in the game more than any others, as it ultimately comes down to the brass tacks of what works at the time and what Sakurai wants to do this generation. Bowser Jr has his fans and, for better or for worse, he's a unique character with his own moveset. His presence is of great pleasure and interest to certain folks, and it in no way, shape or form impinges upon Lucas being in the game.
Lucas is one of my favourite characters in Brawl and, as sad as I will be if he doesn't make it into the game, lambasting Sakurai for his design choices is redundant and solves nothing. If we really want to do something positive with our time and effort, we can appreciate what he has done for us and accept that, for whatever reasons, he just doesn't feel that Lucas is appropriate for this game. There's every chance we may see him as future DLC or even as an alt for Ness; and although I understand this isn't going to please everybody, at the end of the day, I defy anybody to say it isn't an authentic compromise.
This, on the other hand, I agree with and appreciate. I'll grant you that I find the extent to which a series must go before we regard it as a "separate series" is a wee bit arbitrary, but your interpretation is totally valid and I respect you for defending your points.
Now, on the topic of Lucas's potentially being axed from the roster...
Do I think he ought to be cut? No, not at all. I think he's a distinct and interesting character who's similar to Ness on the most superficial of levels only. To say he's a clone is to ignore or disrespect his massive differences, both aesthetically and conceptually, and also to ignore and disrespect Sakurai's ability to create a diverse and distinguished roster. And yet, to say "well Lucina's just girl Marth so that means Sakurai's lazy and doesn't care about us" is truly nonsensical. I'm not accusing anybody here of saying such things, it's more so a general rebuttal of those self-same sentiments that I notice being expressed without sufficient rationale and cogent argument quite distinctly. I love Lucina as much as I love Lucas, and I quite honestly find it to be a personally crass and rather unfair subject to broach: people can appreciate characters just as much as any others, regardless of how their addition to the roster apparently infringes upon the rights and dignities of the characters that they are apparently wholly responsible for no longer being relevant and endearing.
Ultimately, it's not a case of "Lucina / Doc / Dark Pit / Duck Hunt Dog stole Lucas's slot" - that's getting into the whole argument of whether or not "slots" truly exist, and that's a whole 'nother kettle of fish that I won't even touch. At least as far as I can see it, it's simply a case of "these characters are new, let's enjoy them" and it has nothing whatsoever to do with Lucas's exclusion from the roster. We don't understand how or why Sakurai makes the decisions he does; yet he is the director, and it's up to him to make the tough decisions. If he feels Lucas being cut from the game is to the benefit of the game, then, disagree with and be bamboozled by it as we way, it's the director's call and the culmination of the choices he has had to make.
That being said, I don't think there's any reason to think Lucas is out of the running yet. His prospects for the final roster are looking dim, but as has already been said, there's a lot of potential for DLC or as an alt for Ness: don't give up hope on our little PK prodigy just yet, because I'm sure as all hell he wouldn't give up hope either!