One thing I want to point out, before I answer this question, is that "England controlled Scotland" is a bit simplistic. Yes, England was generally the senior partner, but it certainly wasn't dominated like Ireland or even Wales was. They united because Scottish King James VI inherited the Crown of England as well, not because it was conquered. Nevertheless, there is some mileage to the claim. Several Kings of Scotland were forced to be subservient to the English King, the southern Scottish copied English culture (especially under King David), and the capital of Britain was and is London, not Edinburgh.

Okay, so the answer to this question is really a matter of two time-periods.

The first, is why did England and its inhabitants (from the context of England as a unitary state, something that didn't really resolve until the turn of the first/second millenium) dominate the other parts of Britain.

This has three main causes. One, is economic and demographic. England is much bigger and has a much bigger population than the other parts of Britain, meaning that in any war, they always had the population advantage. In addition, it's closer to the continent, making it better at trading, absorbing new technological and political ideas, and so on. Finally, most of England is lowland, while very large parts of Wales and Scotland are mountainous, making farming much more difficult. Even today, the way most people get from southern Wales to northern Wales is by going to England and then back into Wales, because the middle of Wales is mostly mountains.

The second reason is political. Pre-conquest, Wales has only ever been united for 7 years. The aforementioned mountainous geography, plus inheritance laws that split land between sons, meant building a unitary state was very difficult. Fragmentary states meant English conquest was easy. Ireland had a similar issue. For most of its history (both before and after the Norman conquest) it was split between feuding lords (pre-Norman, often known as Kings). There was a High King at certain periods, but his authority over the local lords was pretty weak. Again, this made it difficult for them to resist the more united English (or Normans). Scotland did unite, though later than England, but many Kings had poor control over the Highlanders. Or Lords at all, sometimes: King James VI was, IIRC, literally kidnapped several times as a child.

And the third reason, is the aforementioned Normans. The Normans were one of the most aggressive cultures in western Europe. They were one of the only cultures (pre-Crusade) for whom sailing far away and conquering somewhere on dubious claims (like, say, Sicily, or the Byzantine Empire) was something they'd actually try to do. And they were really good at fighting. They were also considered fairly pious, so in with the Pope. The Pope, for example, actually gave the Norman lords and King Henry permission to conquer Ireland, in order to bring the Celtic Church under Papal control. In a way, it's a slight misnomer to say the English took over the Welsh and Irish. The Normans took over the Welsh and Irish, then slowly turned into Englishmen through cultural assimilation (though saying that, the Normans in Ireland became Gaelicised).

So, that's why the later English became able to dominate the continent. But there's a different earlier question, which is why were the Anglo-Saxons able to dominate half of Britain in the first place, even before "England" became a unitary state? Well, that's still a slightly contraversial question. The traditional view is that highly skilled Anglo-Saxon mercenaries conquered less militarily experienced, disunited Romano-British Kingdoms. But modern scholars are more inclined to view it as a process of cultural assimilation. As it's contraversial, I'll let someone else who understands it better than I explain it.