A nice looking board. And the soldering work appears quite tidy as well, so no worries there.
A couple of comments though:
Firstly, do think about locating the bypass caps considerably closer physically to the power pins. To be sure this is not a gigahertz FPGA, but nevertheless the long(ish) traces from caps to chip don't do any good. This breakout was supoposed to be only for the 2560? In that case you could drop a couple of vias right next to the pwr pins and put SMD bypass caps on the other side of the board - as is usually done.
Another suggestion would be to add power regulator(s) and perhaps a clock/crystal(s) unless you want to keep this as a pure breakout and nothing else. It could make life easier for the prototyper though if this board could handle its own voltages from a generic DC supply. But of course that adds complexity so just a suggestion.
A third and final suggestion would be a separate programming header, either the 10 pin JTAG or in Atmel's case, a 6 pin PDI (2560 uses PDI,right). Lately i have moved over to the Tag-Connect header which is nice because it is a) tiny and b) is not actually a component, just a trace pattern so it saves board real estate without adding cost. Any of these alternatives would avoid the hassle of mesing with individual pins and every so often getting it wrong...