I don't think anything would have worked out well if N hadn't been incorporated into the games. Let's break this down...
Black & White center around a lot of binaries, a lot of dualities. This makes sense because, well, it's black and white. So there a lot of references to this split, "no-gray" world N (and Team Plasma) is trying to go for. You can take this further by applying it to Team Plasma themselves: there are people in Team Plasma who agree with N's words and want a world where Pok?mon are free from the clutches of humans. On the other hand, there's Ghetsis and his cronies. Remove N and what do you have? Not black and white, but just one of them. So much for the symbolism!
In removing N, you also remove one of the things that makes gen 5 stand out from the other games: there's moral ambiguity. In all the other Pok?mon games, the bad guys are all just bad. There's nothing at all to justify what they do because they're just plain bad. Sure, they have reasons for doing what they do, but they're not good reasons. But Team Plasma? Here's something interesting, here's something to make you think. Maybe they're on to something after all. But no N? No dice. They're just your run-of-the-mill, cookie-cutter Pok?mon villains.
And, this is my own opinion here, but I think Ghetsis is thought of as more twisted and evil than the other villainous team leaders because of N. Not only does he want to set himself up for world domination (and is willing to freeze over half of Unova in the process), but he's gone and abused Pok?mon for the sake of manipulating N as a child. He locked up N in a windowless room for his entire childhood and probably most of his teenage years, too. Pok?mon abuse, heavily implied child abuse, disgustingly manipulative, a madman with a lust for power... Removing N from the formula makes Ghetsis not much different from the other "worst-of-the-bunch" villains Lysandre and Cyrus.
I also don't get what you mean by "But then on the other hand he never really did anything hugely important to help your cause or his own for that matter"? Who is "he," Ghetsis? Most of the stuff he did was, purposefully, behind-the-scenes, so we never got a good look at it first-hand. But we certainly saw the results. But if you're referring to N, well, of course he didn't help your cause. Your cause was to stop Team Plasma. And N certainly did do a lot for his own cause. He led Team Plasma, went out of his way to tell you that he was their King... he went out and defeated the Champion all for the sake of his plan!
I'd say one of the reasons why N is so loved by the fan base is because he's different. To this day we still haven't had an NPC with as much depth, as much conflict, as N had. And I'd argue that because of how complex he is, he's the most "real" character there is. A lot of Pok?mon NPCs are so dry and uninteresting and they feel very fake, they don't feel like a real person because of it. But N feels real. He's gone through some awful, awful things in his life, but he pushes on for the sake of his goals. Even though your goal is to stop him, you almost want to cheer for him, too.
He is one of the two chosen heroes, after all.
(And I can't imagine how N being introduced in B2W2 would have made the situation any better. It would just make things confusing--who is this guy with one of the legendary dragons? Why is his claiming to be Ghetsis's son? Huh? I mean, you could add his backstory into B2W2, but part of what makes N so successful is you get to watch him grow alongside you, and the parts about his past are implied, not spoon-fed to you. Part of the appeal of his return in B2W2 was just that--his return. You're happy to see N back because you already got to know him through BW. I feel part of B2W2's success was due to BW's powerful characters setting the stage for the sequels, so if you remove the characters from BW, it effectively weakens B2W2.)
