Here we go with your questions:
2dBi or 5dBi is an antenna parameter, so yes, this will be the only difference between the two modules.
Of course you will be able to substitute the ZigBee module by the Wifi module, though take into account that your code will have to change significantly.
I'm not completely sure to have understood your last question. Do you mean if the Wifi module is integrated in the mote itself? No, it is a separate module, just like the XBee or the Bluetooth.
Please, don't hesitate to ask if you need any help or there is something unclear yet.