I'd like a playable modern day protagonist, preferably the 10 year old Sage. I'd like the Templar scientist attempting to revive the precursor to be the antagonist. The child suffers from has sudden flashbacks of a past life. The mother, fearing the child has schizophrenia, seeks the help of Abstergo. The scientist explains the lore of genetic memories, and the Animus, hiding the side effect of the bleeding effect, and the previous subjects losing their minds and killing themselves. Over the course of the game, the gameplay is interrupted by flashbacks which are vague and cloudy at first, sort of like the Adam and Eve segment from AC2, and only become clear when all fragments are assembled. The true purpose of the game being to uncover "the truth" as to why the Templars are reviving a precursor, the reason being the truce the humans made with the precursor race in the event of a catastrophic event (i.e. the solar flair the precursors predicted), and the leader of the humans having heterochromia (i.e. the Sage). That moment was the birth of the Templar order. The game ends with the boy realizing the truth of his origin, and the Templar scientist swearing his loyalty to the boy in grandiose fashion. Shocker, it's a Templar good ending. Or is it? Rather than the rebirth of the Sage, because of the Animus, the bleeding effect, the boy's mind remains in tact and in control.
Ubisoft creates their trademark open world, but rather than pollute the map with icons and side quests, the game is more dynamic like the Witcher. You come across a seemingly random traveler on your way to a distant town and decide to fend off his attackers, later the traveler opens a shop in that town and gives you huge discounts on items or even a fetch quest that you wouldn't unlock otherwise. Or you could ignore the event and the shop never opens because that shop keeper was killed, instead you meet his wife who offers you a revenge fetch quest. There could be several per town, nothing too excessive, but enough that it significantly affects your playthrough. Instead of "black box" missions with variables, you get that master key from an NPC prior to the mission, or you get Intel of the guard shifts and the guards aren't present during the mission, or an NPC offers to fight with you. Oh, and the assassination missions are not Templars, but rather "Egyptian Gods" that have precursor artifacts. Instead of a scripted mission ending, you have an epic boss fight.
As for the multiplayer, I'd like it to be integrated into story mode. If you opt to play online, then you risk being invaded by other players. Instead of fight clubs against AI, there are multiplayer game modes like Wanted, Assassinate, Manhunt, Artifact Assault, etc. with leader boards that reward you reputation amongst shop keepers to sell the unique equipment that is displayed in their shop but not sold to you until you amass a reputation, like a recipe for fast acting poison that kills another player quicker but nets you less reputation, or a recipe for slow acting poison that nets you more reputation for the kill. You should be able to amass a reputation offline as well.
No micro transactions, season pass, pre-order bonuses (of worthless gear you'll never wear), or scheduled downloadable content. Update the world like GTA Online, with purchasable skins and perks, to keep the multiplayer fresh. In the second season, introduce warrior outfits and agility or endurance perks. In the third season introduce nobility outfits and an extra perk slot. That kind of stuff can be organized by the studio that worked on the multiplayer in the previous gen games.
As far as gang hideouts, maybe implement a nemesis system where thieves, thugs, slum lords, etc. take control of an area and you have to clear it out to amass reputation. The greater your reputation, the stronger and more organized enemies around the gang hideouts get. That way you aren't grinding hideouts with the best gear against low and mid tier enemies, all gang hideouts update or grow accordingly, and impact the economy by making items in shops more expensive.
That's all just off the top of my head.