Some thoughts: (The following should not be taken as an apology for the current state of software development.)
This is nice for security, (because kernel devs have so far failed at building a mainstream kernel which can safely execute malicious userspace software), but introduces significant overhead.
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Qubes OS is an extreme case. But to a lesser extent, all modern operating systems compartmentalize their userspace software, requiring it to live in its own well protected sandbox and communicate through tightly defined channels.
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This introduces overhead and increase latency. Latency cannot be masked by better hardware because CPU speeds are not increasing very much any more.
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