If you've got a better idea for how to avoid the ticking time bomb that is the Sigmarite voting bloc then I'm all ears.
I'm not so sure that it
is a ticking time bomb.
For starters, three votes is not even close to a majority. Then we've got the fact that a really bad emperor can be horrendous for the entire Empire having been firmly set as a precedent. And then we've got the fact that there is
also the extremely strong precedent set that the worst outcome for the Empire (and everyone in it) is the Empire breaking up due to refusing to respect the process for electing a new Emperor.
Given all of this, the dynamics at play currently are actually not bad:
1) Mandred is almost certainly not a contender on account of being a wizard. But this is fine--he's unquestionably heir to the Reikland province itself, which is a huge deal and a big step forward for Imperial wizards. And since he's the legitimate firstborn son of the Emperor, no one can question that he is entitled to the position rather than it being the result of wizard machinations (it couldn't be more legitimate and straightforward if you tried). But by him not making himself a contender, it calms the traditionalists and probably gels well with the Sigmarites, since he'll be formally oathbound to uphold the laws and ideals of Sigmar's Empire and destroy the unnatural evils that threaten it.
2) One of the big contenders is an Ulrican elector count. That suggests that the idea of "Sigmarite candidates dominate" is not at all universal. Being a proven good leader, loyal to the Empire, and a good ruler earns a lot of support and acceptance, regardless of whether or not you're a Sigmarite.
3) One of the other big contenders is a Sigmarite, but not in the church's pocket by any means. The reasons why she's a strong contender are that she's got an excellent, proven track record for fighting the good fight against one of the Empire's greatest enemies (and winning), ruling well in a difficult province, getting along well enough with every significant faction in the process, and a strong track record of loyalty to the Empire and its ideals. The fact that she has also successfully worked with and herded the Empire's battle wizards against the undead is another plus--she's not going to be cowed the moment a powerful wizard shows up. She's unwed, too, which means that she can potentially marry a major Ulrican figure as a way to make the Ulrican provinces comfortable.
4) All of this is hypothetical, because the current Emperor seems to have a bigger issue with the Elector Count of Wissenland than any Ulrican province. He sees the current rift in the Ulrican cult and steers well clear of it, letting them hash out their differences and respecting their boundaries. In other words, a nominally sigmarite Emperor deliberately avoiding even hinting at any kind of primacy in terms of religion or religioun-based authority over a non-Sigmarite cult.
5) The system doesn't have to choose the best every time. It just has to work well enough that the Empire handles its problems
well enough. Sure, you want to avoid having bad emperors (like the previous leader of Kislev literally ignoring all of Kislev's major problems that didn't involve fighting), but it seems like the elector system has been working quite well for a while and will continue to work quite well for generations to come. What the Empire has done remarkably well is
come back from its greatest failures/mistakes/disasters rather than being forever diminished from them. A three-way civil war lasting for centuries? A single catastrophic night that was something of a nightmare scenario for the Colleges? A province breaking away with a massive bribe to a terrible Emperor? An empress-consort that was part of a Lahmian conspiracy? The Empire has come back strong from all of that and more.
Give it some more credit, I think.