The big difference is that the Deck is for enthusiasts. Even though it seems to be a success for Valve (it's permanently sold out, you end up on waiting lists for over a year), the general buyer is a niche but very interested in hardware, computers and also has a Steam account in advance, without which a purchase would not be possible. Accordingly, Valve gives its customers complete freedom to do whatever they want with the Deck. If the customer wants to use a very elaborate application, but the battery only lasts <90 minutes, it's the customer's decision to do so. If the customer doesn't like it, he or she can turn down the settings and enjoy the game longer. But basically, everyone can enjoy his or her games the way he or she wants to. Even I, I would call myself an enthusiast, or at least someone who knows more about this hardware/gaming stuff than the people around me, felt a bit overwhelmed by all the setting options and data at the beginning. However, after some trial and error and reading, you find your way around and there is really the right setting for everyone.
Nintendo would and could never allow this freedom, because the Switch was designed for a customer who doesn't need to have any prior knowledge of hardware and computers. You pick the thing up, play around, and put it down. It simply has to work for everyone, whether they're 5 years old or 80years old, core gamer, casual gamer or no gamer at all.
Even if they seem very similar at first glance, due to the form factor and the selling point "portable gaming" the Deck and the Switch are two completely different concepts.
For me, the Deck works better than the Switch, but millions of Switch owners probably wouldn't be able to do much with the Deck, let alone realize its full potential. There are obstacles and you have to be willing to do a lot yourself if you want to use the Deck to its full potential. The Switch works out of the box and for everyone.
So my guess is no, Nintendo won't follow the Deck in the future.
EDIT #1:
I read again and again that people claim that the Deck only lasts an hour and that is simply wrong and can only come from people who do not have a Deck or haven't played a few days with it. It depends 100% on the user, how long the battery lasts and you can get out as good as always some playtime.
Anyone who has seriously bought a Deck in the belief that they can play todays AAA games with max details for a whole day in the park has unfortunately lost sight of reality. If you took a look at the Deck's data and did the math at the very beginning when Valve announced the Deck, you could already assume that the Deck would be exactly the product which it is now. These bad "surprises" from customers or bad talk from non-buyers can only come from not taking a close look at the APU, the battery, the possible power consumption.
As I said before, the Deck gives you the freedom to do anything with it. If you don't understand that or aren't willing to adjust settings, optimize the experience, and give Valve a hard time for offering too much computing power for too small a battery, then maybe the Deck just isn't for you.
EDIT #2:
I mean, look at Halo Infinite, a 2021 game, running at barely 16watts in medium settings, 40 fps/hz locked. A 100% battery would give me like two and a half hours of playtime.