Regarding the Haven faction, I would:
1. Remove the arrows from level 2 of the guild to the Angels (Why make it so complicated? The connections to Monks and level 1 of the guild are sufficient).
2a. Remove the arrow from the Castle to the Stable (I like the option of building a Stable as in the standard without building other structures + as I wrote before, more than 2 arrows from a building increases its building priority too much).
2b. Remove the arrow from the Castle to the Griffins (They are already the weakest Tier, so they should be built less often - also, if not easier than the Hydras + as I wrote before, more than 2 arrows from a building increases its building priority too much).
3. Make an arrow from the Militia to the Archers, but without an arrow from the Fortress to the Archers (This would be more canonical + a more varied scheme in villages where there is no Fortress).
P.S. Will your racial buildings, such as the Altar of Elements and the Training Halls, be without upgrades?