For me, Sync had at least a little thing to "hold on": the point when you get back to GTVA space when the Shivans come. Transcend has nothing like that - you MUST "fly" with the story.
In what Sync - I'd say - is seriously better than Transcend is the characters. The characters are much more detailed. For me, Transcend - of coure the story made it necessary - was a bit repetitve some times. You see, if capships are engaging each other and we're running for a node, then why do we have to stop and kill a GODDAMN FIGHTER WING? So useless, in my point of view.
I won't say that any of them is bad, I'd gave Sync 9/10, and Transcend 8/10. But, still, this is only my opinion.