Unfortunately the only way to deal with that is to give up on the idea of running on a majority of existing PC hardware and target only a small subset of commodity hardware. Ideally it would all be open, to ensure it isn't going anywhere for a while, but sadly there is no such system.
I'm glad to see I'm not the only one who thinks Users and Groups are the wrong abstraction for systems like this.
2. about web: too bad that design-addict webdev community bloated it. But wish someone make a simpler, faster & straightforward web as portable app platform with few nice commercial qualities...
3. About OS: OS need not be bloated if it isn't running behind popularity by satisfying everyone's remote needs. ( source: plan9, suckless, busybox )...
2. No disagreement here.
3. Unfortunately it still kinda does, because drivers. Two of the ones you listed sit on top of the Linux kernel, which even Linus thinks has become bloated.
Linux above: You need a hypervisor. See L4 or Genode.
Linux below: See unikernels.
An alternative would be targeting a single set of hardware that's likely to be around a really long time. I'd be ok with that and something like a Raspberry Pi, but only if all the hardware was open. Of course, then you're in more of a 68k Mac space where hardware choices are extremely limited.
I think we are talking about a different niche.
If so, no need to think in terms of catch-up. Rather: work out the design values of this niche.
Lots of ideas, but this thread is already deep. I have created #dinghy on irc.freenode.org, would be interested to discuss further.
I like your rule-of-thumb that you should not need a package manager.
Muratori has a theory that USB has made the OS scene complex (https://www.youtube.com/watch?v=kZRE7HIO3vk&t=1350s).
Two other things - the browser and TCP/IP.
Goal: a system where you can fit the whole stack in your head, yet participate in a networked world.
Approach A. Outline a reference hardware platform. Port NetBSD or minix3 or plan9. Then simplify. e.g if unix, get rid of users and groups, get rid of x, get rid of package mgmt, get rid of nfs. You could bootstrap this in qemu.
Approach B. Establish an alternate browser. Something like gopher, but with async events between the 'page' and the user. This allows for chat and form manipulation. You can send non textual content through this async link - video, audio. Codecs are a trap, they lead to pkg management and complexity. How to stop proliferation?