I'm pretty sure Judas Iscariot was stealthy. Unless you mean stealth in the military sense, in which case the Trojan army was pretty sneaky with that horse gift.
But I agree that going that far back might be too far because back then a lot of what made the assassins what they are today probably wouldn't exist. The technology of the hidden blade, the free running techniques, even the irrigation knowledge to grow the hay for their leaps of faith probably wouldn't be around back then.
But this could be an opportunity to see where those things originated, and see how the order was created all those years ago in the height of the Roman and Egyptian empires. We might even get to hear about Julius Caesar's assassination or Jesus Christ's arrest - the ancient equivalent of modern affairs. I suspect the reason they're going so far back is because as the games progressed, so too did the times they lived in. And in Syndicate we reached the Victorian Era. Beyond that, you're starting to get into the modern part of history so I think they ran out of timeline to play with.
I'm also interested to see if the Modern Day Segment of the plot deals with Juno (naturally the answers will lie in Ancient Egypt) and who the main character is going to be. The plot seems to have died along with Desmond Miles.