I'm with Safety Guy as far as the basic principle here; "subtle refinement", not "major overhaul". These are "flagship" knives that work very, very well. I'm inclined to believe that the Native 3 design appeals to a narrower variety of people than the Native 1 does. I wouldn't want to see the Endura and Delica get the same treatment. Subtle ergonomic refinements good. Subtle functional refinements good. Dramatically changing the character of the knife bad.
Now, as to what you _should_ change...In my opinion these models are aimed at the average consumer, not at knife nuts. So my suggestions may be very different from many others here. I don't mean to belittle anyone, I just disagree with a lot of them
Spine ridges: If you use 'em, keep 'em subtle. I like the ridges on the hump of the Paramilitary, and on the butt of the Benchmade Griptillian. Any more aggressive than that, and they get "uncomfortable" in handling. I honestly don't think they add much to the knife, but if done right, they won't detract, and it'll be more attractive to many users.
Larger hole: In my experience, the larger opening hole doesn't make a meaningful difference. Anybody who picks up any of my Spydies can use it easily, regardless of the hole size (and with these general-utility models, gloved use isn't so big a factor as it is with military and SAS-targeted knives). The one exception: I've noticed that some small-handed women have trouble with larger opening holes (but of course, women are a tiny minority of your customers--I've noticed Spyderco has some trouble pitching knives to the female market

)
Finger choil: I love finger choils. All of my favorite folders have 'em, and I'm completely spoiled by 'em. So it hurts to say it, but I don't think one belongs on this knife. A shallow choil (like on the Calypso Jr.) will be a hazard to a customer who doesn't know how to handle it properly, and there doesn't seem to be enough room for a deep choil without dramatically redesigning the handle. I'd leave it off this one.
Adjustable pivot: I appreciate it on the Salsa and Military models, but I don't think the subtle benefit is worth the headaches and higher price on a knife in this price point. And more importantly, I simply don't think the Delica's primary market wants, cares about, or even knows of adjustable pivots. I'd just leave well enough alone.
Full flat grind: I'd love it. But it just wouldn't work without the changes in blade shape that you've mentioned in the past (slightly more belly and thicker stock with distal taper). If you wanted to go through with those changes, and it worked out okay in prototype, then I think it's a great idea. If not, then it's really not a problem as-is. Sure, I love full flat grinds, but the Delica has a thin enough stock that it still cuts beautifully for me. As much as I want a full-flat-ground Delica with a finger choil, it just doesn't make sense from a business perspective. The Delica sells well, while the Calypso Jr. failed. Twice. It's a shame, but that's the market.
(BTW, I sold off my Endura a long time ago, so I can't comment on _its_ geometry)
Redesigned clip: I'd make the clip the top priority on this one; it's the only thing I'd say is "wrong" with the current version. The barrel clip was a great idea, and clip changing with coins is a wonderful touch, but the clip and clip mount just don't _work_ in this model... If a wire clip will fix the torquing problem, then it'd be my ideal solution. It's gentler on cars and furniture, and subtler in the pocket. I like it a lot. If you don't think the market will accept it (the market, now, not the BladeForums community

), then try "beefing up" the clip mount. Or switching to a Calypso-style three-screw mount with threaded steel inserts. But _something_ has to be done about it.
"Deep carry": If you go with the wire clip, just leave enough of the handle showing above the pocket line to get a grip on it, thus eliminating the "wire clips have nothing to grab onto" argument.
That's all I got. Good luck!