I agree, being able to choose which 2 would be awesome.

I believe restricting which weapon abilities are available is a specific balancing mechanic on the part of the devs. Would it be cool to choose? Yes it would. Will it happen? Probably not.

Example: Between (I THINK) v2.0 and v3.0, when the ability to dual wield melee/pistol was removed, I switched from axe/plasma pistol to inferno pistol/plasma pistol. I needed to find something that effectively replaced the #2 AoE attack on the power axe, and the inferno pistol at the time had an AoE attack as it's #2 ability. After posting a few times on the forums here about the great results I was getting with this combo (overheat issues aside) the inferno pistol had it's #2 and (i think) #3 abilities swapped to what they are now, with an armor piercing shot as the #2, and the AoE ability now only available to players dual wielding 2 inferno pistols.

Yes please. 

Some Weapon enchancements work only on the "second" habilities (the ones activated with1 and 2). Its annoying to have them locked when you dual wield

It would not make sense with pistols, as their secondary skills are setup to work when using both pistols.  Laspistols and Inferno pistols for example with their ability of twin beams of death.

If you want the secondary abilities then just equip a second pistol.  While melee is strong, ranged dual wield of pistols is just flat out better.