Whatever you are doing, probably you will not need those extra inputs/outputs. The places where you use many I/Os are e.g. LCDs, graph-bars, LED digit displays, etc. However, if you choose things like Nokia 6100 which has serial controller on-board (
ref) you will use only 4 I/Os on you Mega and probably you will not need more than 10 I/Os for the rest. Just look at MPGuino schematic, it still have some of I/Os available.
For example, if you use GPS, accelerometer, SD card, etc. you will probably use serial communications with them meaning that they will use 2 (COM) or 4 (SPI) pins. Using SPI you can connect multiple slave devices to the same bus. Using 1-wire interface you can connect 5 sensors or more using only 1 pin.
I wanted to get Seeduino Mega as well when I was looking for Mega, but unfortunately it was expensive to get it in the place where I live because of post fees and taxes.
The only problem for me using Mega vs. Seeduino Mega at the moment is that Arduino Mega have access to 6 out of 8 external interrupts. 4 of those 6 included are placed on important pins such as TXD1, RXD1, SDA and SCL. So if you need serial communication then you loose those. But of course you can get around this problem in software, using pin change interrupts or using other 3 serial ports available on the board.