I am aware that the duke of Brandenburg inherited or entered some sort of union with a secularized teutonic order in Ost Preussen but was this land outside of the empire enough to allow them to gain power in their region while other couldn't? Why were they simply allowed to annex land, shouldn't that be a concern for the entire empire? Were they favoured by the Kaisers or something?
I'm not sure what you mean exactly by "outside of the empire enough", however I can explain how Brandenburg acquired East Prussia and so on.
Brandenburg lay at the backwater of the Holy Roman Empire. It had no natural defenses, little in the way of natural resources and was generally sparsely populated. House of Hohenzollern, which were a South-German house controlling area around modern day Nuremberg, bought the title of Brandenburg from the Emperor for a hefty sum. Outside of a large swathe of land, Brandenburg was also an Elector in HRE, which allowed Brandenburg to use their electoral power for favors and prestige.
Since Brandenburg was essentially a poor backwater, with at best a few thousand men as it's army, it had to rely on diplomacy in dynastical marriages to secure territory and safety of Brandenburg. The biggest and most important of these was the acquisition of East Prussia. East Prussia was originally a monastic order of Teutonic Knights, which controlled most of Baltic Coast of modern day Poland. After a series of defeats against Polish-Lithuanian Commonwealth, Order lost most of West Prussia and later on became vassal state of PLC. In 1525, Albrecht von Hohenzollern, grandmaster of Teutonic Order, secularized the order into Prussia. Albrecht was the cousin of Joachim II of Brandenburg, and to acquire Prussia, Joachim married Princess Hedwig of Poland, whose brother later on became the King of Poland. Through this, Joachim II had Polish King name two of his sons as the secondary heirs to Prussia. 4 years later, Duke Albrecht died, replaced by his son Albrecht Frederick. In Lublin, Polish Reichstag declared that if Albrecth Frederick were to die without a male issue, the Duchy would pass to Brandenburg. Which happened when Albrecht Frederick died in 1618 with 2 daughters but without any male heir. Up until then, Brandenburg continued to strengthen their claim to the Duchy, on one ocassion by putting the Elector of Brandenburg as the regent of the Duchy, due to the fact that Albrecht Frederick was of poor mental health.
After acquiring Duchy of Prussia, Brandenburg also acquired multitude of territories in West Germany like Jülich and Kleve through dynastic marriages. On the topic of how they were able to annex these lands, they didn't, as they used marital bonds to acquire these lands, not military means. In fact, until 18th century, the state of Brandenburg was called Brandenburg-Prussia instead, to put importance of both titles. This policy of acquiring territories through marriage changed when Brandenburg was absolutely devastated by the Thirty Years War due to it's lack of military strength, where in Brandenburg lost close to half it's population. Following Thirty Years War, Brandenburg started to heavily militarize in the way we know today.
On the last part, yes, since Brandenburg was an Elector in the Holy Roman Empire, they could regularly use this position to acquire favors from the Emperor. Although they used military and monetary means outside of their position to acquire favors as well. The famous "King in Prussia" title came to be after Elector of Brandenburg supported Habsburgs in War of Spanish Succession. They also used this specific title to not anger both Emperor and King of Poland, who were still technically overlord of Prussia, which they styled themselves until mid 18th century.
Source: Iron Kingdom by Christopher Clark
Edit: One more thing on the "regional power" part. While acquiring East Prussia and other territories like Kleves and Jülich was important, in the end it didn't really made Prussia a regional power. It's administration was still ineffective, it's army small and it's economy weak. It was the heavy and rapid militarization and domestic reforms under Frederick Wilhelm, also known as "The Great Elector" that made Prussia into a regional power, and later Frederick the Great turned Prussia from a regional to a European Great Power.