1. You can't expect them to add all 3 starters in the roster and even then you have to accept that one may be more popular than the other two. The bulbasaur and squirtle lines aren't as popular as the Charizard one, this is a fact whether you or I prefer them over the other. When the decision had to be done it is pretty clear that Charizard was the one destined for being his own character, you may say it's unfair but the dev team isn't obligated to add them for the sake of making them favors; it doesn't mean that the others aren't well liked but they don't hold a candle against Charizard's popularity.
Why can't I expect them to add all 3 starters? They did it in Brawl, and Project M, for that matter. Besides, popularity =/= a good idea. (Just look at the Twilight movies.)
2. What lot do you speak of? The only one comparable is Sheik and that's it. And you can't say it feels redundant because the moveset seems unique so far and besides you haven't tried him yet.
Now Chesnaught is a decent poke but he is not that big in the fanbase, and like I said before, they are not going to choose him just so they can do favors to the character. Greninja is basically the Charizard of the Kalos trio so it was clear who they were going to choose between them.
Lucario: Relatively speedy, charge up B neutral, martial artist, thin, humanoid. ZSS: Speedy, agile, charge up B neutral, thin, humanoid. Sheik: Speaks for herself. Mewtwo: Light, thin, humanoid, charge up B neutral. Are you starting to see the pattern here? And those are just off the top of my head. Smash is saturated with this character type. Chestnaut could theoretically offer a playstyle built around being big and moderately heavy, but also sturdy and good at counterattacking and blocking projectiles. We don't have a character archetype quite like that yet.
3. He is a novelty, yes. But I fail to see why this is listed as an issue. As I wrote before, the guy is only 7 months old so only time will tell.
Why wasn't Blaziken added back in Brawl, despite fan demand and crazy popularity? It wasn't recent enough to be marketable. Greninja is in this to be an advertising push. You admit it yourself below. Some of us happen to care about artistic integrity.
Pokemon seems to get hit with this issue a lot? What? No they don't. That issue is not as frequent as you make it sound. Out of the three you mentioned, only Jiggylpuff's popularity has waned; while Mewtwo, Charizard, Pikachu and Lucario are still a big deal in the pokemon media. Greninja is most likely going to be up there as well.
Mewtwo was cut from Brawl, it looks like the non-overhyped (Yeah, I said it. You wanna make something of it?) Kanto starters have been cut from 4, Jigglypuff remains in despite lack of popularity. How can you tell me with a straight face that Pokemon doesn't have roster issues?
Overrall it was a smart decision to include him, the guy is in the new pokemon games and he is Ash's starter in the anime, it was a logical choice. You said that they didn't think it through, but a few sentences ago you suggested Chesnaught; not a bad pokemon character choice but a sure way to shoot themselves in the foot considering that Greninja is the most liked. So yeah, we gotta consider that stuff.
So basically, you're saying that Smash should be a popularity contest, and only fan-favorites should get in? Then what the flying fish are Wii Fit Trainer, Mr. Game And Watch and ROB doing here? Why was Fire Emblem included in Melee despite being a Japanese niche series at best at the time? Why is Ridley still not playable?
There are several series that I only got into enjoying due to Smash highlighting them when I wouldn't have given them a second glance otherwise. Smash is a place for all Nintendo All Stars to shine, and constant fan-pandering just leads to rehashing the same ideas over and over again.
I never said that Greninja is an inherantly bad character. I think he looks pretty fun, considering his faults. I'm just sick of seeing the same old popularity contest win the day, when there are other, more unique and creative options left at the wayside because "OMG NINJA!!1!" In the long run, what's creative and original will stand the test of time, beyond what's hip and trendy. That's why I'm bugged that Greninja is in. Short term, he looks nice, long term, I can't seem him lasting the test of time.