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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.
I may be tempted to go custom next time I'm in the market for a cross frame, if just to specify a rear triangle with ridiculous mud clearance. Other than that I think I'm a traditionalist so it'd be pretty much mk. 1 with cantilevers.
Just picked up a wound up cross fork from eBay. Those things are not light - it weighs the same as the budget, alloy steerer(ed?) Ritchey fork it is replacing. Nice ride though.