By breaches you mean these agencies own a ton of exit nodes?
Not just exit nodes, but guard and relay nodes as well. If they control all hops in the circuit, all your anonymity are belong to them.
You can increase the number of hops to make it very difficult. Guard nodes are pinned, so they might know who uses and who doesnt use Tor (doesnt matter if you arent using a bridge).
You can also set up your own exit/guard node and configure Tor accordingly. While not a recommended setup, it works pretty reliably.
Do you suggest that we trust our ISP instead, and pretend that they aren't compromised by default?
what's the alternative to Tor?
Physical world. Lol
More specifically, couriers to hand deliver your messages, like Al Qaeda had.
There are no real "alternatives"; but see I2P, Lokinet and Freenet for some other options.