I kinda hate myself for doing this but here's my fanfic-esque Season 4 plot structure:
1 - William returns (same as the one we got)
2 - Skid is built
3 - Skid's maiden voyage, replicas are discovered
4 - Replica #1 is explored
5 - Replica #1 is destroyed, a hint regarding Franz Hopper is discovered
6 - A Franz Hopper investigation episode
7 - An Odd/Aelita character episode, main plot still progresses a bit
8 - An Ulrich/Yumi character episode, main plot still progresses a bit
9 - Replica #2 is explored
10 - Replica #2 is destroyed
11 - An Aelita/Jeremy character episode, main plot still progresses a bit
12 - Replica #3 is explored, XANA William is materialised, his weakness is discovered
13 - Replica #3 is destroyed, William is saved (and he can't be possessed by XANA randomly anymore)
14 - A William character episode, he's afraid to rejoin the team.
15 - Another William character episode, he rejoins the team, everyone's still pretty hesitant
16 - Replica #4 is found & destroyed, it's revealed XANA has hundreds of replicas
17 - William episode with Odd & Yumi, new Franz Hopper clues found
18 - William episode with Aelita & Ulrich, final Franz Hopper clues found
19 - Franz Hopper is saved and materialised, a copy of XANA William shows up for the first time
20 - Franz Hopper bonding episode
21 - Franz's secrets are revealed, Project Carthage and all that, big flashback
22 - Project Carthage plays a role in defeating XANA so this episode focuses on finding it (it was relocated at some point), the Kolossus monster shows up, XANA manages to delete the "Return to the Past" program for good. Gotta raise them stakes.
23, 24, 25, 26 - Big finale - Ulrich fights the Kolossus, William fights XANA William, Franz Hopper gets a Lyoko Avatar (some sort of fancy wizard maybe? The kind that can summon meteors), etc.