Yes, I think future games should have version exclusives. It's part of the core game and should never change. The original intention for version exclusives was so that one person buys one game, and the other buys the other. At that point, the two friends play and trade with each other.
With GTS, Bank, and casual trading, it gets even easier. You can buy a single game these days and with a little effort, can easily build a living dex regardless of exclusives. Removing version exclusives just gives players another reason not to interact with one another, and that's counterproductive.