If you were to consider The Subspace Emissary canon (I'm sure you don't, so shut up. This is hypothetical), both Twilight Princess's Link and The Wind Waker's Toon Link end up meeting each other sometime after the end of the game, whenever you go add Toon Link to your big party.
The timelines are probably going to stay completely separate. That's logical based on how they came into existence in Ocarina of Time. Most of the games so far seem to be on the same side of the timeline as Twilight Princess, so it would be cool if they added to the story of the Wind Waker timeline. As far as we can tell, Spirit Tracks is going to do that.
At first, the splitting was probably only partly a copout. They also had to find a place for Hyrule disappearing after Ocarina of Time's events to fit. By now, I wouldn't say it's any sort of copout at all, since Phantom Hourglass and likely Spirit Tracks are expanding upon it.