I know, but having only having the top a touch screen with the bottom of buttons will just look... bad

Better battery life, lighter system, more money to spend on the chipset or main display, more space for a more powerful chip, cheaper cost, more room for a real second analog + bigger buttons all-around ... 

I say ditch the second screen. It's useless in like 90% of 3DS games anyway and there would be many, many benefits to doing so. 

I'll take a cheaper, lighter system with better controls and a better chipset than having a second screen for the sake of having a ... second ... screen.

It's basically preferences, really but I really like two screens. Unlike the Vita, where the system is really wide, you can get a more narrow and compact handheld. Two screens may not be necessary if 90% of the games, but it still has some useful functionality (adding a map, menu) where it is in more convient location. You can get some really awesome ideas for screen splitting like TWEWY. Maybe, because I got really use to playing games and viewing two screens at the same time or consistantly, but it can be really handy.

Why would the system have to be wider? They could still use the same clamshell layout if they really wanted to, just no bottom screen. 

I don't think people realize too the bottom screen really limits what Nintendo can use for a chip and limits the size of the battery they can put on the bottom side of the portable too because the screen hogs up a lot of space. 

That said the Vita is honestly more comfortable to hold than any 3DS model IMO. They really nailed the ergonomics with that one more or less. 

Next Nintendo handheld will do fine, but not that good compared to other Nintendo handhelds
As for Sony, I'm sure Vita is their last handheld

If there was only one screen for the next handheld, it would most likely be a touch screen. Therefore, we would have the top screen be a touch screen while the bottom containing the buttons, joysticks, etc. But this design doesn't look good anymore more and as you said, the clampshell design is less ergonomic than compared to the Vita so if Nintendo goes to one screen, its most likely going to be a Vita/GBA design without a clampshell

Pokemon alone could guarantee Nintendo handhelds a modicum of sucess

The future is uncertain, that is all I can say ...

People should stop insinuating whether they do or don't have a future since it's too early to tell ...

Software is irrelevant if Hardware is not present.

Pokemon= Future for HHs. There is your proof