I have a very black and white look on this "dilemma", which I feel isn't really even a dilemma to begin with. It can be a bit uneven, but it has its balances.
New & Noteworthy definitely tends to highlight more longform series, with a lot of the gag comics showing up in Best New Webcomics. Best New Webcomics was honestly built for gag comics, because BNW was built to be picked up and scrolled through without needing context. All the comics in there are simple things you can just read and enjoy in less than 5 minutes, and there is very ever rarely the threat of spoilers, or being thrown into a random context-less story. You can read it on the bus to work/school, during a walk, while you're working out, whatever it is. It doesn't require much effort, which is the way it's really supposed to be, because it was built to draw you in with quick and easy reading so that you could delve into the rest of Tapastic and enjoy the other features it has to offer.
New & Noteworthy is great for highlighting longform stories, because then you can start right from the beginning and know what you're getting yourself into. Even I've used N&N for this several times in the past and I use it all the time now to keep up-to-date on stories. There are a lot of awesome series that have made it in here.
If the longform stories don't show up in BNW, then that just means you (you as in the creators, myself included) are gonna have to work twice as hard to get it attention, which you should be doing to begin with, because it's not Tapastic's job to spoon feed people readers through their filtered sections or put you (as the creators) in their specialty sections just because you wished for it hard enough.
Because - as harsh as this sounds, I know - in the end this all boils down to everyone's personal feelings of, "My comic isn't popular enough, I blame the design of the site for not giving it the highlights I think it deserves!" And in the end, there are still so many comics that are great, but probably never will make it into those sections, just because Tapastic is constantly growing every single day in readership and creators, and unfortunately, not everything is going to get the moment it has to shine even if it does deserve it (and I've seen some of these series firsthand that are just wonderful, but didn't have the luck to get to where other comics on the same levels have).
And I'm only saying this because this has been a recurring issue for a long time now and from the start I know that's what it's been about for a lot of people. Sure, maybe not all of you, but out of the creators, at least 99% of you (myself as well, because we all love our publicity).
Tapastic can only do so much for you. And out of what they've done, it's a hell of a lot. So if your longform chapters aren't making it in BNW, do what you can to get it in N&N or the "What's Popular" section. Talk about it on Facebook, talk about it on Reddit, Tumblr, Twitter, Tapastic's forum, -anywhere-. We can only blame the design of the site for so long before it starts getting redundant. Work harder, work smarter, continue to grow, and just do the best damn job you can do.