I would rather like to see a dex that structures the Pokemon in evolutionary lines (and purportedly we'll be getting lots of [pre-]evos for old Pokemon, so going with this plan only makes more sense). That would be the default dex, and it would integrate previous generations of Pokemon within it once you expand the capabilities of your Pokedex. However, the National Dex would still be present in the game and you could switch between this reorganized dex and the National Dex.
As for the features from the other dexes, integrate the most useful/standard features, give the Pokemon fairly stocky dex entries, and add some other useful features. I'm thinking the type-searching feature from GSC, and perhaps searching which Pokemon in the dex can learn certain TM moves.