The save/reload issue becomes a non issue if sovereign death is unavoidable. That is to say, Sovereigns can (and absolutely will) die from old age.
Suddenly the idea of succession is viable and important, and strategic choices regarding your dynasty must be made game-years in advance. Succession wars become possible. Traits revolving around succession become viable. Marrying off a daughter stops being the most tactically retarded thing conceivable.
The only thing you have to give up for all of this benefit is the idea that your initial Sovereign is immortal and is "you". Honestly, I don't think the players are connected enough to the Sovereign to care. I know I'm not.
IMO the entire idea of dynasties is completely worthless if your Sovereign is immortal.
Now that's a compromise I can get behind - it completely changes the situation. Currently, we have an immortal, invaluable, irreplaceable sovereign - if he dies, how many will continue playing as the heir when they can reload and try again? Some, yes, but not enough that succession should be a priority I think.
On the other hand, if no matter what you're going to lose the sovereign eventually (it just might happen sooner if you take some risks with him), then taking risks and accepting his death if it happens is a much more reasonable proposition, and probably not an automatic reload for most people. In this case succession becomes an essential part of game balance, something you want to think about not only for your own kingdom, but simultaneously worry about how your enemy's/ally's succession will work.
A separate idea, not necessarily related: what if marrying off children had non-negotiable, involuntary diplomatic repercussions? You'd still of course choose when to marry them off, but you'd have to choose carefully if it initiated a binding alliance. Say I marry my daughter to your firstborn son, now as long as he's the heir (or even the ruler, after you die), your nation is automatically allied to mine, sharing enemies and refusing to turn against me (we are relatives, after all, my daughter is involved in your court politics and influencing your leadership in my favor, just like real life!). If she dies before having an heir and your son remarries, or the son dies before having an heir and succession passes to someone else, all bets are off - I no longer have any influence over your line of succession. If she does have an heir, we're inextricably linked as long as my bloodline controls your line of succession. This isn't irreversible, of course - you could deliberately kill off the inconvenient heirs that link you to a nation you're no longer so friendly with, it'll just cost you the units themselves and probably provoke war.
This could lead to some really interesting situations - what if your second son is married to a third nation, my enemy? They might go out of their way to assassinate the heir (i.e. the one married to my daughter who favors my nation), so succession passes on to the second son that they can influence, turning you against me. The politics could get very medieval European/Song of Ice and Fire-ish. Keep in mind you only have to let this direct your politics if you want to - nothing would force you to marry off your heir, indeed I'd hope you'd think twice about it first, and you'd always be able to send a diplomatically inconvenient heir on a suicide mission. Ideally a smart AI would take advantage of such a system and try to pressure you into an arranged marriage to seal an alliance, but you'd still have the choice.
Also, keep in mind that the "marrying the heir = forced alliance" idea is not dependent on having a functional succession system or a mortal sovereign as mentioned previously; marrying the heir could have diplomatic consequences even if he never actually inherits (the game could track the line of succession, i.e. first in line for the throne, second in line, and so on, even if inheritance never happens - in fact I think it already does/did at one point in beta?). This of course reduces the heir from "future you" to "pawn in the political game," but that's not so bad - still makes for a very interesting political system.
And a word on sons inheriting - it may be the classical European way to only consider sons as heirs and ignore daughters until you run out of sons, but there's a way to give players the option of having daughters inherit equally (i.e. oldest child is heir regardless of gender): just tie it to the Egalitarian trait. Perfect, isn't it?