There's still barely a difference between the two. The reality is, there will probably be 20-30 Pokemon unique to the individual titles, and, along with that, there'll be differences between encounter rates of some species.
Other than that, the main difference is the title screen, default character names, and where/when you encounter the legendary Pokemon available in both versions.
With the existence of Wifi trading, as well as the GTS, a system that lets you put out a Pokemon on the net for a specific trade, it's wholly and completely unnecessary to buy both versions to collect every single Pokemon.