When that's what you're working with, you're limiting yourself quite a bit in terms of adding new security solutions. At best you'll be at least a decade behind the innovators in security who aren't afraid to build new stuff from scratch and break the old stuff.
Making security the primary goal of your operating system would be nearly as perverse as making swapping the primary goal of your operating system. The primary reason security seems special here is that we do have working swapping in our operating systems, but we don't have working security.
Nevertheless, if you try to add virtual memory to an operating system that was designed without knowledge of how such a thing could work (like nearly all 1960s operating systems) it is going to be pretty rough going! Today, security is where virtual memory was 50 years ago.
Qubes is interesting especially because it doesn't break compatibility with everything else.
There's been some exciting progress in the formal verification department in recent years, though.
I critiqued QubesOS in the past over re-inventing the wheel and on a highly insecure platform. Her recent write-up supports my critique more than ever. Regardless, they're at least doing something with provable benefit and high usability on a platform with proven benefit, both of which can be further secured or extended by others. An exception to the rule of mainstream INFOSEC where the sense of security is almost entirely false as no effort is taken to address TCB.
The only project in this space leveraging best practices in TCB or architecture is GenodeOS. They're doing what I suggested QubesOS do a while back: build on all proven, low-TCB techniques in academia. Main critique I had of them is they're too flexible and need to focus on a single stack long enough to get it working solidly like Qubes team did. They stay building on and integrating the better stuff out of L4 family of security engineering research, though.
That's just a tiny selection from my collection. Lots of exciting things going on for secure and correct tools that are still powerful. Postgres and Common LISP are both weak and boring in comparison despite being good tools. :P
I mainly consider solutions like Qubes to be for preventing accidental leaks, containing damage from regular malware, and making recovery easier. Much like the Compartmented Mode Workstations and MILS virtualization that came before it.
Real, more-thorough security will break compatibility or take a huge performance/functionality hit. Was true in any system designed to high assurance or surviving NSA pentesting. Will be more true for whatever supports legacy applications on today's more complex, leaky ISA's/API's. CheriBSD is closest thing to an exception but I don't even trust its monolithic parts due to how attacks can jump around in a system. Nizza Architecture on non-Intel, security-enhanced processors is best model for now given we can at least isolate security-critical apps into their own partitions on tiny TCB's. No mature FOSS implements that, though.
So, regular malware defence with Qubes, etc and energy-gapped systems + KVM's + guards for high-strength attacker defence remain the options.
Are they all so much more secure by design that you consider them to be great projects?
My experience is heavily with server-side web languages, so I'm particularly skeptical of those. Even the most secure-seeming web languages have buggy, insecure implementations at first.
Note: This comment is mainly for others reading along. Something I do on forums. I know you already understand this point.
So "most" is probably okay. with a couple noticeable exceptions:
Android needs to get its shit together. Not letting any old manufacturer write device drivers with jaw-droppingly bad security holes would be a start. I last looked at vendor-provided drivers in 2010 or so and I very much doubt they have improved.
(A while ago I wanted to store a secret on an Android device. And I couldn't do it. Ten year old platform and no effective secure storage; did the ghost of J Edgar Hoover visit Google and threaten them?)
Network equipment manufacturers: Why even bother with a home router when some code monkey stuck a hard-coded password into the firmware? I'd love to be able to inspect the code on the device I'm trusting to keep my network safe. Interesting that DDWRT is under political attack, isn't it?