The modern equivalent to System/38, IBM's POWER hardware running IBM i still has the same benefits. I actually really like the concept and the way the ILE runtime works, but it's too bad that much of the platform is stuck with legacy design decisions and hasn't been modernized.
I agree with about everything you said. The System/38 design was one of the best cathedrals of old. Very forward-looking, thorough, consistent, and great for admins of the time. Still the only capability system bringing in revenue. Adapted pretty well to modern stuff but main OS's issues & stagnation hurt it as you said. I think the fact that it's pricey and proprietary kept the OSS innovation out, too.
However, the change to the AS/400 and POWER cost it one of its greatest features: hardware-enforced integrity at the object level. That's the feature that would still be giving hackers hell if it was widely deployed. The Intel i432 APX and i960MX had similar property. Interesting enough, IBM actually has secure CPU's they've prototyped and even sold to select customers. Would be great if they integrated one with IBM i at microcode, compiler, and OS levels. That plus an optional interface for new customers without legacy crap would be a huge differentiator that might give it new life.
