My recommendation against the mega is two parts. One is price, the second is certain shield comparability. I didn't look closely enough at the data logging shield you mentioned. The SPI pins on a regular arduino are pins 10-13 and the ISP header. On the mega, they are 50-53 and the ISP header. Thankfully the ISP header is in the same place on both boards. You will have to check the shield to see if it has the ISP header so you can use it. Also on the mega, the I2C pins are moved. Typically it is not a big deal to run the wires. It is just something to keep in mind. (I2C would be used for RTC or other devices)
If you need all those pins, go for it. Otherwise there are a lot of other boards that might have something to give you a jump start.
An arduino/Xbee board you might like is the seeedstudio stalker. http://www.seeedstudio.com/depot/seeeduino-stalker-atmega-328-p-600.html?cPath=79_80
Check around for a reseller closer to you.
It include a micro SD slot, a RTC and battery, and a XBee socket. I have one and like what it has to offer.
My recommendation to check out synapse isn't for my benefit. I really think you will like what they have to offer. The Radio modules have 20 General purpose IO Pins, 8 of which can be used for ADC. They have two serial ports. But, there is not an easy way to log to a SD card directly on the rf engine that I know of.
Good luck and please let us know how your project goes.