Change this line in the Transportation rule:-

If the target Territory is controlled by another Country, it cannot be moved to.

To:-

If the target Territory is controlled by another Country, this is called Invasion Transportation (or simply Invasion), which can only be done from an adjacent Territory which is controlled or occupied by the invading Country. Invasion Transportation lasts an indefinite number of periods (use ‘?’ to represent the number of periods in the “In Transit” section). In order to make an attack post at that Territory, the invading Country must pay for a period of Invasion Transportation there, which costs the same as Hostile Transportation plus 1 Metal per unit. If the defending Country loses control of the Territory, the attacker may reduce the number of periods to 0 and thereby complete the Invasion.

And add this to the Conflict rule:-

In the case of an attack method used in the course of an Invasion, the population units being moved in that Invasion Transportation is considered the attacking presence.

A Country performing an Invasion may also use a special type of Attack Method, Invade, which is effective against all Government types. If the attacking presence is greater than half the defending presence, the defending Country loses control of the Territory, which then becomes disputed. Each Fortification in the target Territory doubles this requirement.

Ok, so the invasion has been weakened in many ways: the aggressor must maintain control or occupation of a neighboring territory (allowing for defensive counter-attacks that disrupt this supply base) and invasion attacks cost a bunch of metal, and there is no more double effect for native-population-specific abilities.