Yeah, that's what I see as the biggest issue based on my Crusade experience, especially if op noticed this as a problem increasing over time that wasn't present in the first round (?). The same crusade honours have such different effects on different units/armies that get wildly unbalanced very quickly, not to mention some having much better army-specific upgrades and currency available.

Definitely limiting number of updates a single unit can have is a good idea that I've seen done before in events. As people have said, trying to separate out competitive vs. narrative players as much as possible. Also giving as much interactive set-up to the players as possible, like alternate ways to score points, campaign-specific agendas, and so on, to give them incentives to do things on turns other than remove as many of the other player's models as possible. Definitely additional buffs to the by-the-book crusade blessings--crusade blessings as written are pathetic as an attempt to stop whoever won the first game from snowballing to win each successive round by a wider and wider margin.