Board Thread:Game Discussion/@comment-88.215.34.158-20130510151236/@comment-8284783-20130510184646

You are better off leaving them separate, because trans-scanning itself costs money, and the card, once trans-scanned, will actually add less exp as an upgrade than if you were to feed both cards separately.

Also, regarding your first question about weapons, there IS a bonus for a character using their signature weapon. Aside from the fact that you will obviously automatically get all three other bonuses (faction, class and specialization), you will gain an additional 15% stats boost. These % boosts are added to whatever the weapon might be giving at base, and applied to your character's base stats. All of that is then multiplied by the position coefficient (X2 or X3, depending on whether your character is in the front or back row) and THEN, an additional 15% and 30% will be added to that ATK value if your character is trans-scanned or max level, respectively (or both if it's MTM'ed).

The fact that the % ATK bonus is applied separately from the % stat bonus from weapons makes it better (since it's multiplicative as opposed to additive) and is why you should always strive to MTM your better cards (and probably also why you shouldn't bother with anything that you will end up replacing :D).