Atmega2560 AVCC decoupling
Well in theory, with decoupling, more is usually better (although at some point you get diminishing returns). This actually involves two different issues, Decoupling and Bypassing. You can find out more about them here, but basically Bypassing is about getting rid of noise from the supply, and Decoupling is about being able to provide short bursts of current. Technically L4, C10 and C13 are more dealing with Bypassing, while C12 and C11 are Decoupling.

In the reference design, those capacitors are more meant for Decoupling, although of course it has an effect on Bypassing as well. The type of capacitor isn't specified, but it should typically be ceramic. 

The decoupling for the two designs is basically the same, so the difference is the Bypassing. Using a 10uF capacitor instead of a 100nF capacitor will definitely be a bit better, but using an inductor as well will be much better. It turns the RC filter formed by the trace and the capacitor into an LC filter, which is a second order filter and has much higher attenuation at higher frequencies.

I don't think theres a question of whether your design is higher performance (it is higher performance), but there is a question of whether it's worth the extra cost and board space, and only you can really answer this as it depends on how precise you need your ADC readings, and what environment your board is in etc.