For a couple of reasons. First is that the kit (I assume you're making a kit) has hops provided, and once you add your malt extract to the water, the thickness of the wort will affect how much bitterness you get from the hops. If you boiled all the water at the same time, your beer would be a bit more bitter, because of better hop utilization. Also, chilling 2.5 gallons by cooling it and adding cool water is an easy way to get the wort down to fermentation temps. If you did a full wort boil, you'd need some kind of ability to chill the wort. And finally, most beginners don't have a 6+ gallon pot to start, but many have a 4 gallon pot.