There is a lot of legacy cruft in x86, but it's the devil we know. After decades of use, we are still discovering vulnerabilities, in a platform thought to be well-understood.
The closest alternative would be ARM. In any case, it's a massive undertaking.
It is not obvious to me that it's the design warts of x86_64 (wholeheartedly agreed--I don't like x86_64 either) are the cause of the security problems we're seeing. Other architectures also have speculative execution and multiple rings. It's a lot easier to avoid vulns that are a consequence of increased performance demands when performance is not the primary reason people pick your platform.
On the contrary there's SPARC, MIPS, PA-RISC, POWER and a whole heap of others that perhaps were written off prematurely. Need to move quickly tho' while some vestiges of expertise still remain.
Sparc, Tilera and Parallela are unfortunately gone. I had high hopes into the latter two, esp. since Grid CPU's are perfect for machine learning. Much better than GPU's.
The closest alternative would be ARM. In any case, it's a massive undertaking.