Using two sabers in combat is clearly inferior to using a double-bladed saber in almost all respects, but it seems that there might be some benefits. In particular, crystals that give certain benefits outside of hacking and slashing might stack when used in two sabers.
For example, the Etaan Crystal allows for a 1 Innate Talent (Parry) Mod and a 1 Innate Talent (Reflect) Mod. These would obviously be beneficial even if on the offhand blade while the primary blade held a more offense-based Crystal, but what if the character had two Etaan Crystals? This should stack and allow for an effective 2 free ranks of each talent. Not too shabby.
An even more interesting option comes from the Corrupted Crystal. Wielding such a weapon offers a free dark side Force point, so a pair should offer two such points. This is a great way for a "low FR" character (like many of the losers that became Inquisitors) to claim the power they need to take on their better.