Inherent Bonuses and houseruled feats/powers/items are a biggie for me and any game I have or will run.
It would be really swell if the houseruled items have options for interacting with the builder in a reasonably user friendly fashion, even if it means modelling that stuff after other "objects" that are already in there.
I can already do this by adding custom files to the hacked CB classic, though I do have to play around a lot with kludgey XML. What it means though, is for me to switch completely, the Vecna builder is going to have to keep up, I'm afraid.
And that brings me to refluffs. I should be able to refluff powers names and effects indiscriminately. All of that junk should be an editable text box, even if only on the character sheet side. I use MSE because neither builder does this. The output from MSE is quite nice and it has a relatively gentle learning curve.