A clamshell design would be better suited for another handheld-only revision of the current Switch, but an immediate question is how to integrate sticks that double as a button in order to be compatible with all games. A clamshell essentially forces circle pads in place of sticks.
Integrating a second battery in the top half is a stupid idea. It would increase the thickness of the device considerably while adding weight to the half of the system that isn't being held with the hands. You'd need some very sturdy hinges for that, but aside from that, the console would be too heavy to be comfortable to hold for longer play sessions (everything above an hour).
Since you'd have built-in controls, the chipset and battery all located in the bottom half, you'd have to make big concessions to the size of the battery. That's the reason why the Switch Lite revision opted for the wider design instead of a clamshell. As technology and battery efficiency improves, you could eventually make a Switch revision with a clamshell design, but for a new console it just wouldn't work because you'd either have a system that is too bulky or comes with atrocious battery life.
From a marketing standpoint, you'd also have the problem that you'd be making a handheld that connects to the TV because the console would have to ship with a separate controller for TV usage.
Legend11 correctly predicted that GTA IV (360+PS3) would outsell SSBB. I was wrong.
A Biased Review Reloaded / Open Your Eyes / Switch Shipments