Look EUIV (or CKII) is not a good representative of medieval or early modern history. Those are game mechanics which highly simplify complex socio-political and legal situations. You don't just push a button. An annexation, for example, isn't just about conquering the land. Take the example of Wales in the thirteenth-century.

The earliest 'English' claim to 'Wales' (which as a term Wallia is a foreign Latin creation) was supposedly established when Alfred the Great, not an 'English' ruler but king of Wessex received some form of submission, and possibly tribute, from the Welsh rulers (note plural, it was very rare for a Welsh ruler to 'unite' Wales). Between the ninth- and mid twelfth-centuries the rulers of 'England' (in reality the lands which 'controlled' those that bordered Wales, on which the Marches had been established in the second half of the eleventh-century by William the Conqueror) were perfectly happy exacting tribute from the Welsh. When Henry II came to power in 1154 the situation changed somewhat and he attempt, but failed, to extract a more total submission from the Welsh rulers (of Gwynedd and Deheubarth, two of the principle Welsh kingdoms). His attempts floundered due to numerous competing interests and the confederation of Welsh rulers after Henry's victory in 1163.

While the English traced their auctoritas over Wales back to Alfred they were in no position to enforce it, nor it fact might it have ever existed. We have no legal treatise detailing under what conditions the Welsh had submitted to Alfred. Between the period 1170 to 1197 the Welsh had negotiated (in various different manners) peace pacts with the English crown, which had included English grants and marriage pacts with Welsh rulers, and peace agreements of a more general nature while Richard I was on crusade in the Levant.

In 1197 the most powerful Welsh ruler Rhys ap Gruffudd died (I discuss the political context of Wales here) and King John, who ascended to the throne in 1199 was able to capitalise on the situation. This didn't mean he immediately declared his ownership of Wales, despite being in conflict with numerous Welsh rulers and 'supporting' the claims of several others who came to do homage at Poitiers on 3/4 December 1199.

Instead John forged a fairly firm alliance with Llywelyn ab Iorwerth of Gwynedd in 1201, which included the marriage of Llywelyn and John's illegitimate daughter Joan in Oct. 1204. For the rest of the decade John and Llywelyn remained firm allies, but John's politiking in Wales (which I discuss here), especially with Gwenwynwyn ab Owain Cyfeiliog of southern Powys, led to a falling out between John and Llywelyn. It was at this point that John established a pivotal agreement with Llywelyn. If Llywelyn died without a legitimate heir by Joan then his lands would escheat to John or his heirs (ie. the English crown) except those granted, by the king, to Gruffudd (Llywelyn's illegitimate son). This seems to have been the charter that Llywelyn demanded during Magna Carta (Clause 58) and probably destroyed. As it happened Llywelyn had a son by Joan, Dafydd, who was did homage to his nephew Henry III in 1229, whereby he was confirmed in all the rights his father legally held. Unfortunately, this was a rather ingenious piece of legal chicanery, as Llywelyn had, between 1215 (Magna Carta) and 1240 (his death) created a soft empire within Wales. Henry's receipt of Dafydd's homage only obligated him to honour Dafydd's rights within Gwynedd, not all of Wales. There were those, within Wales, who were supporting Dafydd's illegitimate brother, Gruffudd's, rights to a portion, although not necessarily an equal in status or value, of Gwynedd. Dafydd imprisoned his brother and soon rose up against Henry. By 1241 Dafydd had been crushed and he was forced to revive the clause that, should he not have a legitimate heir, his lands (ie. Gwynedd) would escheat to the crown, except those granted, by the king, to Gruffudd, his brother, who was now imprisoned in the Tower of London. Gruffudd actually died trying to escape the Tower of London in 1244 which caused the Welsh to rise up. The war was particularly brutal and Dafydd died without a direct heir (ie. a son) in 1246. However, as David Carpenter has pointed out, the treaty had not made provision for this. Now Gruffudd's children, Dafydd's nephews, inherited portions of Gwynedd. The second eldest, Llywelyn ap Gruffudd, managed to defeat his eldest brother Owain, imprisoning him for the next twenty-one years, and solidified his control of Gwynedd. As the crown weakened in the run-up to the Baronial Movement of Simon de Montfort in the 1260s, Llywelyn ap Gruffudd made major movements towards extending a confederation-based authority in Wales and eventually, at the Treaty of Montgomery (1267), Llywelyn swore liege homage to Henry III and received the homage of all the barons of Wales (an act typically seen as the creation of an 'arch of kings' - a feudal structure with the Prince of Wales as feudal subject of the Crown and the lords/rulers of Wales as subjects of the Prince of Gwynedd.^1 )

For a while everything seemed rosy, although the confederation that Llywelyn had built was shaken when an important ally, Gruffudd ap Gwenywynwyn, lord of southern Powys, plotted to murder him in the early 1270s. Alongside this conflicts over jurisdiction escalated with the Crown and in 1277 Llywelyn rose in rebellion. It was swiftly and brutally put down by Edward I. There was, as yet, no indication that Edward I had any inclination or intention to annex Wales, this was made especially obvious by the enquiry he commissioned post-1277 on where the laws and customs of Wales were applicable and where those of England or the March were applicable. However, Dafydd ap Gruffudd, Llywelyn's younger brother and agitator during his reign, began another rebellion in 1282 which Llywelyn joined. During the rebellion both brothers died and Edward I annexed England after another brutal invasion in 1282-3. He issued a modified version of the common law and announced the formal annexation of Wales to England in 1284 in the Statutes of Rhuddlain.

So there you go. That's how an annexation occurs, with 'personal union' elements included pro bono.

^1 This is, in part, a subject of my research and may be disproven - once I have a more substantial body of evidence.