I think it would be a mistake to assume that Meltdown/Spectre are somehow obvious and should have been spotted early in the design process. Remember that these vulnerabilities have been preset for 10 years and only now have people found them. If the issues had been spotted within the first year of CPU release you could argue that it should have been more obvious to the designers as well.
Eh, a lot of it has to do with how we use computers have changed.
The x86 world went from either single user systems (Windows 95) or multi user trusted code systems (Business systems that run their own code) to multi user untrusted code systems (VMs that execute javascript from the internet). Many mainframe systems have had much better code/cache separation because they were specifically designed not to leak information between multiple users. These systems were also far more expensive than even the most expensive x86 systems.
