Learn English – Yeah, no | What does it mean

You are mistaken in supposing this to be a recent innovation: to the best of my recollection it arose in the late 1950s. At that time it was supposed to be characteristic of the ‘beat’ community, but it entered youthspeak almost immediately and has been current among the young ever since, at least in the United States (I cannot speak to other dialects). As teenagers grow older and are called upon to address more diverse audiences more formally, they generally learn alternative expressions (as it were, so to speak, I think, in my opinion) culled from severer registers; but like never entirely disappears from speech with close friends.

It has a useful and indeed essential function in speech as a discourse marker. When it first arose it was employed primarily as an anticipatory emphatic, to signal that what follows will be of particular importance—Maynard G. Krebs’ favorite expression was “Like, wow!”—but by the end of the 60s it had acquired additional anticipatory uses: notably 1) as a signal that a subsequent pause will not mark the end of an utterance but further processing and 2) as a lexical ‘quotation mark’.

There is thus nothing to deprecate in the usage except snobbish preference for more prestigious markers. If the usage annoys you, I suggest you seek a more pretentious class of interlocutors.

The "Speak English" normally refers to the listeners inability to understand the (English) words said by the speaker - in your example due to lack of technical knowledge.

In the movie, Captain America woke up after 60 years so there are many things he does not yet understand. He could ask Stark or Banner to "speak English" when they would be using technical jargon not understandable by "normal people"

In the case of Stark, it is used in the opposite manner. The sentence

heavy ion fusion at any reactor

shows a level of technical knowledge that pleases Stark, who is highly technical. His reply shows he is happy to meet a clever group member and he is being sarcastic towards the rest of the group who he feels are his intellectual inferiors - in particular Banner's Alter Ego who barely speaks English.