I'm curious why you believe this, outside a few watering hole attacks, and the (now-patched) CMU attack. Given a known-good entry guard, where is Tor broken?
https://www.usenix.org/legacy/event/leet11/tech/full_papers/...
https://www.torproject.org/projects/torbrowser/design/
There's probably a more specific statement from the Tor Project that I'm forgetting at the moment that sets forth the idea that you should only use Tor with Tor-aware client software (that controls what privacy leakages may occur at the application layer).
Consider we have that system wide tor proxy instead of the torbrowser bundle. Now exit node operators get all your TCP traffic. It's fine if one knows what they're doing[0], but if that was the default way for the average user to get on Tor? A privacy and security disaster IMO. Not only would we not provide mediocre privacy, we'd actually endanger people.
[0] and you've got proper stream isolation, which I'm not sure how possible it is system-wide with unmodified software
There are VMs that do that but still wouldn't recommend that to someone that doesn't understand tor and networking. Even inside such a VM you'd still use Torbrowser.
It combines Tor and app-level security/privacy measures in an accessible way.