Which one to use?

I'm probably not the right person to talk about the pros and cons of the new Midi Remote; I haven't studied it thoroughly enough for that.

What I do know is that the (midi part of the) Cubase plugin and the Midi Remote are mutually exclusive. The Cubase plugin is built to learn from Cubase, while the Midi Remote is built to learn from the device. When the Generic Remote is deprecated, neither of the parties can learn from the other, so I cannot see any use for (midi part of) the Cubase plugin. The key command part of the plugin may have a future life, but not the midi part.

My personal opinion is that the Midi Remote is not yet a finished product (Cubase 12). This may very well be a misconception due to too little study of the Midi Remote, but I have found it too limited whenever I have tried to use it. Steinberg claims that the Generic Remote will be deprecated but that this will not happen until the Midi Remote can do everything the Generic Remote can do. I would guess that we will see at least two major Cubase updates before that happens.

From my point of view, the situation isn't "Cubase Midi Remote vs. the Stream deck plugin;" it's "Cubase Generic Remote and the Cubase plugin vs. Cubase Midi Remote and the Midi plugin."

The Cubase plugin is built to be simple to use but has limited features. The Midi plugin is built to be very versatile but is a bit more "complex" to configure. There is no doubt that a future solution with the Midi plugin and (a fully featured) Midi Remote can do much more than the current Cubase plugin/Generic Remote. Since Stenberg plans to deprecate the Generic Remote, that's where everyone will end up; the question is only when.

My recommended approach depends on your situation.

If you are using the Generic Remote with either the Cubase plugin or the Midi plugin today (and are satisfied with its functionality), I see no reason to rush to replace it with the Midi plugin/Midi Remote. I recommend that you, somewhere down the line, start looking at the Midi plugin and Midi Remote and examine what they can do. Maybe you find the new possibilities worth the effort to switch.

If you aren't well accustomed to the Cubase plugin or the Generic Remote, I recommend that you skip those. The Midi plugin/Midi Remote is the future-proof combination, so put your effort into learning and configuring those.