I think org-mode is good. But I think that it and markdown could have better syntax for links. Like a link doesn't have to be wrapped in an opener or closer, since any spaces can be escaped. So you could simply do:
A main goal of Markdown is to be easy for anyone to use. Having to substitute characters in a URL string might be fairly trivial for you or me, but certainly not for everybody.
It's a trade off definitely. The way I think of it is, how often would you have to sub? Rarely. Since most uris do not have spaces, and even putting a URL in an address bar will usually sub it.
On the plus side, having a simpler syntax for URLs I feel is more readable which is great for ease of use. I think ~ looks like a link, and @ makes sense semantically.
But to be sure I think the legacy syntax could remain as a fallback / alternative. New syntax is something that could be tried in a flavor.
~A new search engine@https://google.com
I think considering the status of @ in the rfc this can be parsed. If a link has spaces just replace them with + or %20