Your assumption about how damage dice are added on a critical hit is incorrect. You double all damage dice. Per the 5e SRD:
When you score a critical hit, you get to roll extra dice for the attack’s damage against the target. Roll all of the attack’s damage dice twice and add them together. Then add any relevant modifiers as normal. (5e SRD, pg 96-97)
Note that the rules specifically state that any extra damage dice that are part of the attack, such as a rogue's sneak attack dice, are also doubled.
If you are in fact referring to the barbarian class feature Brutal Critical then you may have a point.
Let's look at the text from the SRD:
Beginning at 9th level, you can roll one additional weapon damage die when determining the extra damage for a critical hit with a melee attack. This increases to two additional dice at 13th level and three additional dice at 17th level.
From this, we can see that you can add one additional weapon damage die when you determine the extra damage for a critical hit with a melee attack.
Regardless of the weapon damage dice, the rule says add one additional weapon die.
To begin with, you are swinging a 2d6 greatsword. You roll a 20, and double the dice, making this 4d6. Brutal critical says, add another weapon die. This brings it to 5d6. I believe this is both the intent and the way it is written. The designers had to know that barbarians might be swinging big weapons that start with two damage dice, and wanted barbarians to have that extra edge when they score a critical hit.
Thus, at level 9, a barbarian gets to add 1dx of the weapon's damage die. At level 13, this power gets even better and the barbarian is rolling 6d6 for a greatsword. At 17, 7d6.
Now, let's compare the alternate option, the greataxe -- a weapon that does 1d12. The greataxe on a crit does 2d12, and in the hands of a level 9 barbarian adds another 1d12 bringing it to 3d12. Clearly, 3d12 has a higher potential damage output when compared to the 5d6 (3d12 max = 36, 5d6 max = 30). The greataxe also has a slightly higher average damage output on a crit, 20 vs 18.
This advantage grows all on the way up to level 17 when you're adding 3 additional damage dice for the brutal critical, with the final advantage being an average of 8 more damage for the greataxe on a critical hit.
On the other hand, if you're not focusing on critical damage, in the long run your 2d6 greatsword will average out to do a hair more damage overall (7 damage vs 6.5 avg on the greataxe).
Regardless of the weapon used, the ability is clear: It does not say double the damage dice, it says to add one additional weapon damage die, and any additional damage dice are on top of the normally doubled critical damage.