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I haven't clogged a frame up around the brakes with wide stance cantilevers and a high straddle, it's always around the bottom bracket junction for me.
I've never actually tried drop bar hydraulic brakes, just had bad experiences with bb7's, so I'm not dead against them. The hydraulic brakes on my mountain bike are great, so despite my previous statement I would consider them. It'd just mean two new wheel sets as well as a discs and a custom frame. Not going to happen anytime soon anyway.
Doesn't mud clearance become less of an issue with disc brakes?
Full hydro disc brakes are pretty awesome.