Don't understand how they will continue the story line in the present without Desmond. Just saying with no spoilers.
Doesn't Erudito sync all of Desmond's DNA memories to the "cloud", which as stated in III by William and shown in Project Legacy, can be viewed by anyone? --- PSN: MrMonochrome UMvC3: Hulk / Vergil / Spencer, SSFIV:AE: Dudley
Even though they won't have desmond they can still use his father. He would have access to all the same ancestors as desmond. Personally I would love to the next game be set in civil war era america. With an expanded wilderness that is similar to red dead redemption (not nearly as big but you get the idea) That would be a great next installment.
Don't understand how they will continue the storyline in the present without Desmond. Just saying with no spoilers.
Desmond is dead, but his body is still there. The Animus uses his genetics, not his thoughts. Just put the body on life support and you can continue on endlessly without worrying about warping his personality.
I still think it's likely that Juno will have to take over his physical form, since she doesn't have one. It's not like they bothered to find Eve and give her a female one.