For me personally, I'm ok with two World Championships and I'm ok with a unifcation at some point. If I had to pick one or the other, I'd probably go for unifying the titles at this point.
Since brand exclusivity for Raw & SD! is pretty much dead, and has been really for almost a year now, so, on the surface, having two World Championships no longer really seems to be necessary. Allegedly, however, one main of the main reasons why they've kept the titles separate is the belief that SD! having its own World Championship helps sell tickets to house shows. I think there's some truth to that after all. When's the last time the WWE had a house show in which a World Championship wasn't on the line?
While the brand split is pretty much dead, the WWE is still ultimately able to, usually, run two different house shows in two different areas a day. There's no reason why they couldn't keep doing so without the WHC but, again, the WWE feels that each brand needs its own top strap for house show purposes. There might be some degree of truth in that. SD! is already viewed as the less important show as it is, so taking away their World Championship might only further that view.
But, to be honest, I'm sure WWE could come up with some idea that could work. One less World Championship could mean that SD! could really be used to put a huge spotlight on one of the mid-card titles.
If a unification does happen, which I do think it will at some point, then I expect one of two scenarios:
1. The WWE Championships absorbs the World Heavyweight Championship with the WHC ultimately being retired. The WWE Championship has always been the top title of the company no matter what. The odds of WWE doing the opposite are damn near astronomical as the WWE Championship is the title created by Vince, Sr. almost 50 years ago. That title is linked to the history of the company in a way that no other title on the roster is.
2. The WWE & World Heavyweight Championships are unified into a single, brand new championship with its own lineage. This scenario is also unlikely, but one that I do like to some degree. Vince is going to have to step down eventually for one reason or another, so the creation of a brand new World Championship, maybe calling it simply the WWE World Championship, could be seen as starting things off fresh. This would create a lot of buzz and interest because wrestling without the WWE Championship, in all honesty, is something that many people would never happen.
I don't look for either title to be gone for a long while, but I do believe it'll happen someday.