Double reliability, double performance, half price

This $7 gem does all of the above:

Consider:

• Two 3-cell 20C 1300mAh LiPo = $13.98 (= 2600mAh and 40C discharge)
• One 3-cell 40C 2650mAh LiPo = $24.50

By hooking two half-size batteries in parallel, you get twice the discharge rate while total battery weight stays exactly proportional to total capacity.   Cost savings can be significant, as both larger and higher discharge rate batteries are more than proportionately expensive.

Less obvious advantages are perhaps more important:

• You now have redundant batteries, doing nothing else doubles your receiver power reliability in the event of battery failure. 
• If you split a BEC off of your ESC battery power connector, you now have a redundantly powered BEC supplying power directly to the receiver, even Rx's that do not have redundant power inputs.  ESC failure is no longer catastrophic.  This eliminates the argument that the external BEC may be as likely to fail as an ESC's internal BEC.
• Batteries are half as strained at the same level of performance, so they should last longer
• Batteries may be more flexibly arranged for balance/CG/space constraints
• You can have two flyable battery sizes instead of one (e.g. 1300mAh and 2600mAh)
• You can also have three flyable sizes if you split asymmetrically (e.g. 1000mAh, 1600mAh, 2600mAh)

There is no need to match battery sizes, but you do have to match the cell count.  Parallel batteries will always drain together, their voltage will remain matched as they drain.  The down side of having a large and a small battery hooked in parallel is that the larger battery will be supplying the majority of the current at any given instant, meaning that total discharge rate is increased but not fully doubled.