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We are somewhat unfairly not including them in the "actually designed" category, even though you, from direct experience, know HERO/Champions is. I mean, why don't I exclude HERO, because I'm only familiar with it in the context of emulating superhero stuff. However, I have a lot more experience with GURPS (albeit only up into the early '00s).
I'm going to snip a lot of your response, for a couple reasons, but I want to respond to a few things about it.
I think its absolutely legitimate to argue that both GURPS and Hero are not ideal for every job, ironically for opposite reasons; Hero was originally designed as a superhero game, and GURPS was originally designed as an elaboration on In The Labyrinth, and thus for more or less gritty fantasy and modern gritty action. As such, the farther away from those you get, the more heavy lifting is needed with either of them. In addition, they have fairly opposite approaches to genre support; Hero really wants you to use the tools at hand to construct what you need, and supplies the minimum number of additional rules needed to cover ground its superheroic bones don't properly handle, while GURPS is generally a believer in adding whole new subsystems and other things to bolt on.
I also think the suggestion of naive design (in the sense I believe you're using it) is at least a defensible position, since Hero was first designed in 1981, and GURPS in 1986. There's obviously been considerable design water under the bridge since then, and while the systems have been refined multiple times since then, their basic design principals haven't, and they've been in some ways very conservative in their refinement (to the best of my knowledge a metacurrency was not officially introduced in Hero until its 6th Edition (and if it was prior to that, it was 5th), its still optional and very clearly an afterthought).
That said, I have to note that your experience with GURPS is showing its age. So is mine as far as that goes (my experience with the newest edition is very limited), but is a bit fresher than yours. That doesn't mean your experience was illegitimate in the time frame you're using (the overuse of the core GURPS magic system was absolutely a thing) it just means its ignoring the evolution of the system (even the prior edition of GURPS provided in supplemental materials at least a half dozen different magic systems of pretty wildly different sorts).
As such while there's some relevance and legitimacy to you considerations, you're overstating it because you're largely talking about decades old versions of the systems, and some of your objections have been addressed.
And of course there are more modern generic systems that one can argue about the design, but one can't suggest they're naive EABA and Savage Worlds come to mind (ironically, they have a philosophy similar to Hero and GURPS respectively in terms of genre support, though they come from different focal points than either of those).
SECOND EDIT - Total aside, but do you have any insight into why Champions went for this pretty complex/fiddly "squad combat" motif in its combat design (particularly stuff like segments)? I'm guessing it was before your time and my presumption would be that it came out of familiarity with various wargame-ish concepts, and as such I would characterise that as "naive" design, but perhaps the actual thing was that they wanted a highly tactical superhero game, not one that emulated the genre and its tropes and so on.
Some from column A, some from column B (and no, it was not before my time; technically my involvement with the system predates the existence of the system as such, but that's a long story not relevant to this thread). Also, you have to understand there were large parts of that which were what they thought of as emulating elements of the genre. As an example, the phase/segment system was designed to represent things like the generic tendency for supers, no matter their basis, to be able to be far more reactive than most mooks and agents are in the genre (which is why you have things like the speed gap between them. The fact its very fiddly and tactical was based on the perception that since combat takes up so much of a typical superhero comic's "landscape" that it
should be detailed and very interactive (see my comments about medium mattering). Now, can you these days argue something more narrative like Supers! RED with its much more narrative focus is more appropriate for the genre? You absolutely can. But you have to
make the argument, and part of the argument turns on how important the game elements of RPGs is.
TLDR here is that while its obvious that the design
is naive (in the sense that it didn't have a lot of other models to work from), its not
thoughtless; most everything was done for a reason, and the reasons were seen as appropriate things to represent the genre as seen by the people involved at the time.