I think separate lines (subs) would have been fine. That's how they originally were. Enough people seem to think highly enough of their favorite for it to be plausible.
I think the interest in the original lines is reflected here. In the very very beginning, it took some time to gain momentum. Eventually it was a beast, and ultimately died out due to more interesting things being made.
If we look at it in that light, MotU was first, and carried the most interest. PoP leveraged that interest, and separated into two lines, and was clearly marketed as such. No need to stop MotU, but add a girls line in it as well. If you liked MotU, good, buy 'em, if you wandered over to the other toy isle and found PoP and liked 'em, great. Interest was clearly dying, so they revamped into NA. Also branded differently but leveraging what worked best... He-Man. But it wasn't the same for some, while for others it came at the right time and was their jam. NA was the end of the road.
Most people are at the top of the funnel, and further down you go, the more people drop off. The Great Rebellion was branded differently from MotU, the Horde was not. The Horde ladies more associated themselves to MotU in this way, and let's face it, the Horde, just like the Empire and Cobra have an evil cool factor built in.
PoP did have rooted hair. So what you say? Well, they also came on different cards, all looked the same in different colors (no two-headed, big handed, long snouted, skull faced gimmick that could match MotU), had differnt body structures (not going ~there~), and other than a commercial for a cartoon, had absolutely nothing to do with MotU. So when people mention rooted hair, don't get your undies bunched and blame the sexual insecurities of the KIDS who are now us.
Which do you think TMNT collectors would most likely have in their collection, April O'Neil or the troll doll turtles? And the rooted hair O'Neil is not the version I'm talking about.
PoP, as a toy, was NOT the same as MotU. Deny that all you want, but as you do, maybe step back and look at it. Look at some Christmas wish books and old TV commercials
The cartoon is a different but similar story. I'll try and make it shorter, and you can just read into it. He-Man, and the Masters aired. Great, people like it. Make girl toys and incorporate them into one cartoon, we can't afford two. Great. Okay, now try making it more futuristic and change stuff around and call it New. Done. You loose the initial interested party when you do this, but it's a gamble to gain more traction, and it did gain new tradition. And the interests were different as well.
I know some people stuck with it all. Some saw the end and it led them to research the beginning, but for the most part, that young of a target audience doesn't give you that wide of a window. There interests develop and mature fast enough to outgrow one thing after another. This can be seen with 8-back fans and later wave fans. To each their own.
The people interested in the 2009 line-up, probably aren't as interested in the 2014 line-up. It's just... not the same, even with Two-Bad and Modulok, and even though ~they're all the same now~, because they're not. It's that easy of a complication.