I think any changes should include a medium-term trial run. Once people get over their initial, "Oh no, they messed up ENWorld," fears and give themselves time to get used to it, it will not seem so bad. Then again, if it is bad, it will be easy to change back without too much fuss as long as the changes happen in manageable steps.
So what is the #1 non-d20 system out there anyway? And do they really not have a few leading websites of their own already?
I'd much rather see a new forum for each d20 game system (although I think there are too many of those already too) rather than non-d20 games for now. I'd like to see a Spycraft specific forum myself, but I think AEG is already doing or going to do that.
I'd look for any games that already don't have a good website out there first, or games that are too new to have a good site.
As almost a second thought, why not just provide a good links page for each game first. Including other RPG games would expand the news coverage on the front page--I think that would fragment the currently exclusive D&D/d20 audience to a certain degree. Nobody wants White Wolf news in their d20 news. But if you don't change the news page, then you aren't really covering the "other" games.