This is still from limited experimenting on all chapters, and my opinion may change, but here is what i chose for now:
Chapter 2- Definetely naval expertise. The demons don't have artillery to snipe your towers ( although now that i said that, they may receive some in the next update) so having a good defensive line to stop their attacks is very nice.
Chapter 3 - Now here my choice is split between if i want a melee, or a spellcaster army, so it varies. Mostly i would go with pack of the bloodclaw, but since it would get repetitive after a while, the predominantly spellcaster army with academical knowedge, would be a nice option if i want to try a new strategy.
Chapter 4 - One of us all the way! I know when to pull off elites form the battle when they are at low health, so the extra health isn't needed for me. That 10 damage though, it makes him so much more worth the price.
Chapter 5 - I definetely like shadows of the shadow master a lot more. That attack speed makes golems destroy building a lot quicker, marksmen killing air a lot faster, cavalry going even more berserk combined with charge, and that's pretty much it.

Chapter 6 - Naval expertise. I don't really like bonus regen as an thing to have.
Chapter 7 - Again shadows of the shadow master for the same reasons i stated in chapter 5.
Chapter 9 - Order of the holy bastion. I think your regular troops are durable enough. Plus the paladins becoming a even better heavy units is a thing i would definetely chose.
Chapter 10 - Chosen of the high king, the improvement on your rifleman is already nice, but the unlocking of the shieldbreaker, a very good tank and heavy unit, makes this bonus eclipse the holy bastion by a lot ( a lot or no golden guard hate may have made me chose this)

This is where i think it would be a nice time to stop.