You cannot choose your heirs in MTW. The only method open to you is killing off the runt before he ascends the throne. Known affectionately as "pruning" this can be carried out in several ways:

1) Spies can be dropped on a low loyalty prince to have him framed for treason and put to death. This is the preferred method. If his loyalty is not too low, repeated attempts at a treason plot setup will lower his loyalty even more and also give him traits that will have the same effect. He may also gain valour vs spies as part of these traits however forcing to give up and employ an assassin...

2) A decent assassin can take an inbred, secret pervert, coward out of the equation. Failed assassinations will gain him traits vs assassins but won't lower his loyalty.

3) The inquistion can be called in as a last resort if you're a catholic faction. If the target has low piety he should be out of the game fairly quickly if hit by a 4+ star inquisitor. Failed attempts can cause totally opposite traits, such as "true believer" or "atheist" so it can go either way. If the Inquisition keep trying they should get him eventually though.

4) One way boat trips are the emergency procedure. Just ensure the target doesn't have a port and don't pay the ransom and you won't see him again.

To try and avoid all of this, try to keep an eye on when your heirs are about to mature. Get your king out taking provinces and winning battles to gain influence in readiness, as the better inlfuence he has the better quality heirs he will produce. Also remember that while relieving besieged allies often seems pointless it does gain your king influence every time.