As it's designed, I'm sure you know there's not much to do because it's only a growing number, and that severely limit potential options.
Make it grant tangible bonuses, like you tried with vassal limit bonus. I'd still stick to that, if on a much lowered scale so that it only matters for the player and the odd very successful family (either capping at a low number, or each threshold being exponentially higher on a preset but not complicated formula).
That, or make it trigger potential choices or events, unless you design a whole mechanic around it I'ìm afraid there's not that much to do with it :/
Using it as a point of comparison could be viable, so the relative difference could be more important than the absolute number. For example, if you give a title to a character with little to no dynasty prestige, vassals with a considerable amount of dynasty prestige could be angry, while if you give it to someone with high dynasty prestige they won't be, and if you give it to a member of their dynasty, they'll like you. That way you'd be encouraged to land your own dynasty members (as your dynasty likely has plenty of prestige), and dynasties of powerful vassals. Similar things could be done for marriage and assigning guardians, so characters would prefer marriages to prestigious dynasties, and for their children to be educated by someone from a prestigious family.
This could all be coupled with or partially replace the effects of personal prestige, and basically be a mark of powerful or influential families. Characters could be made to be more willing to join factions or plots led by characters with higher dynastic prestige than their own, and even more so if their dynasty prestige is higher than the target of the plot or faction. Extending that, it could also boost their chances of increasing their dynasty's power, by upping the odds that characters from prestigious dynasties would be able to more easily gather hosts and become adventurers. Also, I had posted an idea in the suggestion forum involving using dynasty prestige as a factor in selecting new patrician families in merchant republics, instead of generating them from nothing, for example.
Back on marriage, perhaps dynasty prestige could also be improved by marriages to more prestigious dynasties, with the boost being present so long as their is a link between them. That would make a marriage good at first, with surviving children locking it in so long as that line survives. Then, if there are enough links, the dynasty heads could have the option of forming a long term dynastic alliance.
Adding or linking more mechanics to dynasty heads could be useful as well. I've had good luck in linking the ability to ask decadent characters to straighten up to the dynasty head, for example. Perhaps dynasty heads could be asked by dynasts for support if they are running low on cash, or if a dynast wants to become an adventurer.
Within the dynasty, there could be plots and negotiations for who will be the next dynasty head. This could be a space for branch families within the dynasty, perhaps. Each branch could have its own head, and they could compete to be the overall dynasty head in a similar manner to how patrician families compete to become the next ruler of the republic. (And if a branch of the family becomes powerful enough, having over a certain percentage of the overall dynasty prestige, the branch head could choose to become semi-independent and turn his branch into a cadet dynasty.)
I think I'll repost this post in the suggestion forum later, so it doesn't get lost.