This is incredible work so far! I really like the way you've structured the first episode. I generally don't use walkthroughs for Assassin's Creed games, but I'm overwhelmed by the side quests and map locations in Origins and Odyssey.
For me, it's important to know roughly in what order the main story and side quests unfold so that I have a plan of attack in my head. The Origins walkthrough is mostly great and really detailed, but I find it hard to understand what side quests I could or should be doing next.
With that in mind, my suggestion is a hybrid of the ideas: have a page for the main story and list each side quest inline, either as it becomes available or at the end before you move to another island, without the side quest walkthrough there. Then, have that list entry link to the island specific pages where you provide more detail on side quests and locations. In that side quest list on the main story page, you could include especially important info for certain side quests, e.g. "Really hard and would be good to come back to later when you're level X" or "Good for grinding out progress towards X miscellaneous achievement" to help the reader identify when it makes sense for them personally to flip to the island page.
Using the first episode as an example, I see it working like:
Episode 1 - Another Day, Another Drachma
So It Begins
- Hungry Gods
- Merciful Gods
- In the Footsteps of God
- Mercenary Work --> Good time to unlock the "Make It Your Own" achievement
Debt Collector
- A Fight With Talos
Where all quest names are links and side quests are differentiated by a hyphen. After that roadmap, you'd have the main quest walkthrough with just the links to the side quest walkthroughs where you think fits best (either after a particular story mission or all at the end before you leave the island).
Regardless of how you choose to do it, I'm impressed with the work you've done and look forward to reading the walkthrough.
