You can't "execute ANY content
natively on any platform".
It is true that the things that you list are the actual problems, and there are many others, too. The modern WWW is a too messy design, and additionally to that, web pages and web browsers are also badly designed.
I had partially written specification of "VM3", which hopefully will be an improvement for cross-platform application programs. There is no CSS, nor Unicode (well, technically you can include Unicode text fragments, but it is discouraged), and it is independent of protocols (so you can use with local files, DVD, HTTP(S), Gemini, etc, but none of these are required nor is it limited to any specific kind). All I/O must be done using extensions (identified by UUID), which require a specification; it also has a mechanism for polyfills which is (in my opinion) superior than that of WWW. Furthermore, is intended better for the end user controls/customizations. Also, some of the internal design decisions I have done differently due to things that I think are better than what are currently done (e.g. how linking works, and many features use a binary format, etc). Extension declarations can also be linked with each other, too (note that this is linking the interface, not the implementation; the implementation is deliberately not specified by VM3).
Some VM designs are good for interpreted, and some are good for JIT, but I think that to make implementations competitive, and improve efficiency, it may be better for the design to be good for both, so that is what I have tried to do. For example, there are restrictions on how branch addresses can be derived (e.g. one feature is that you cannot store branch addresses in general registers).
VM3 cannot "execute ANY content natively on any platform" (and nor can anything else), but my intention is to make something better than existing systems.
Things similar to TerseNet, and other possible different things people will want to make, some of them may be possible as specific subsets of VM3. An implementation of VM3 can then support specific subsets or can have full capabilities (preferably, configurable by end user).