How to actively prevent becoming the junior in a personal union in Europa Universalis IV?

There is no way to actively prevent a PU besides not engaging in royal marriages. There is always the possibility to end up junior partner in a PU, if you have no heir, but active royal marriages, this is increased if a potential senior partner shares your dynasty.

However, becoming junior partner isn't all that bad. You have three options to regain your independence:

1. If you are strong enough, you can declare an idependence war pretty much immediately. In fact you can declare this war at any time, even while fighting in a war with your senior partner for ultimate backstabbery.

2. If the senior partners ruler dies and has negative prestige, you become independent. This is hard to influence, but maybe possible by causing him to lose wars.

3. If the senior partners ruler dies while your country has a negative opinion of him, you are independent. This sounds easier than it is, there aren't many ways to reduce the opinion of your people vs another nation.

There two very easy way to prevent becoming a junior partner in a PU passively.

Be at war.

It's not possible to inherit a country that is at war.
(I loose the commonwealth inheritance because he was lock in one of those never ending wars the AI loves so much, even birding did not seems to work).
Of course, if you are at risk while your ruler is 15 and sterile, it might be long. But you only need to keep it until you get an heir, or until the current ruler dies.

Have your own juniors.

Way more difficult than the first one, but on he other hand, you will be protected for a long time.
To get confirmation, start a game as France, and look at Provence.
Provence starts the game as a Valois without heir (the starting day it might says that Provence have an heir, but the heir will mysteriously dies the next day). Yet, even if you Marry them (your first quest anyway), you will see that they will get a random Valois as a ruler if the current dies.
(Sames goes with Aragon)
I don't remember if it works with Vassals
Edit : in the 1.23 version, Provence keeps it's heir at the start of the game, same as Aragon. The global trick still works, but not this way to check it.

Of course, none of those option does not protect you of aggressive inheritance, but if the IA is trying to aggressively inherit you, you are in a very bad situation anyway, and it might be a blessing, because it means that it can kill you.