Hmm.. Well I do own a 3DS, and have put well over 200 hours into it since launch. All of your ideas seem solid, except....
Headphone jack on the right side of the system.
Yeah, this would be not so great. It would get in the way of your grip on the system. Maybe you could position it so the cord runs between your fingers, but you couldn't guarantee that it wouldn't get in the way of everyone's hands since everyone's hands are different. Maybe you could put it near the top of the bottom shell, but then you would have to move either the volume slider on the left or the wireless switch on the right. You couldn't have it any lower on the side, because you would lose access to it while playing (because it would be underneath your knuckles as you're gripping the system). You can't put them on the bottom, because you would have to release your grip on the system in order to mess with any of those buttons, which is why there are no inputs on the bottom edge of the bottom shell. Also, putting the headphone jack at the sides would increase the length between the jack and your ears, giving you less room to maneuver your 3DS when you have to move it for gyroscopic game features (AKA aiming the bow in Ocarina 3D, which is awesomeness)
Stop, Select and Home buttons that glow in the dark.
"Glow in the Dark" compounds need to receive light during the day in order to excite photons that will glow at night. That would not happen if the 3DS was closed and/or in your pocket most of the day.
Better speakers and organic LCD screens.
OLED? I like my 3DS under $300, thank you. Nintendo will not take a loss per unit for this.
Volume slide equivalent to the one on the first DSi system.
The clicky software buttons? Besides the obvious, I hated those because you couldn't adjust volume when it was closed. Like I want to bust out my 3DS for a second when my wife isn't looking, and suddenly I hear "Heya, itsa me, Mario!" just because I didn't reach those stupid software clicky buttons in time.
Stereoscopic 3D slider replaced with plus and minus symbols on the bottom rightside of the top screen.
It actually is on the bottom right-sided of the screen already. Unless you mean on the actual hinge.
Better Online.
You know, it seems like when a lot of people say this, they mean stuff like Xbox live, with cross game chat and stuff like that. Maybe on a home console, that may be desirable, but on a handheld, when I'm trying to fill 5 minutes waiting in line for something with some Alpha Bounce, the last thing I want is to get a message from someone I know taking up my play time. "Dude, you're playing Alpha Bounce? That thing is crazy." Yeah, you just took up 33% of the time I had to actually enjoy this game. If I wanted a text message, I would use my phone.
And on that note, I don't think online on a portable is the best thing in the world. Chances are, when you're out and about you're not going to be in Wifi range anyway, and even if you had a 3G Vita, it's not fast enough for realtime online play, and you wouldn't want to pay for the data plan anyway.