It's more about who the instructor is, than what agency. You can have great instructors from lesser known agencies, and crap instructors from the best known one(s)...
I think that agencies determine a whole lot of the curriculum so much so that it is a given that what you learn is largely determined by the course structure laid down by the agency.
E.g. from my very limited experience:
Safety stops
PADI - 3mins at 5m
UTD - Min deco
How deep you can go on air
PADI - 40m (or in theory 66m or 1.6 PP02)
UTD - 30m max. No deep air dives.
Air sharing
PADI - Pass octo to your buddy. Drill ends there.
UTD - Full S Drill + Ascent with all stops. Swimming with donated hose, buddy on left, buddy on right, buddy in front.
SMB Deployment
PADI - Cursory demonstration. Only one person in my class got to actually try it in the water. After that, has no memory of how to do it. I never got to touch the SMB in water.
UTD - Drills on SMB deployment on land. Detailed instructions on where to hold reel, how to setup, etc. SMB deployment drills in pool. SMB Deployment at depth in the sea.
Toxing buddy rescue
PADI - No training at OW and AOW level
UTD - Training on buddy rescue at OW level
Propulsion methods
PADI - Only taught big flutter kicks
UTD - Frog, modified frog, helicopter, back kick
There are lots more things I feel are determined by agency that are really beyond the control of the instructor. As a consumer I find that choosing the right agency is crucial to not only your competence but your safety (e.g. safety stops, deep air, etc.)
---------- Post added December 23rd, 2013 at 04:01 PM ----------
Oh yes, one more big difference that I forgot...
Dive planning
PADI - Taught to use tables / calculator to determine SI and pressure groups. This was in theory only, we never did this in practice, and none of the PADI trained divers I know even remember how to use the calculator thinggy 6 months after getting the C card. I found out as I was trying to verify something and asked around, as I have also forgotten how to use it.
UTD - What is the max depth? What is my NDL at this depth? What is my rock bottom pressure / turn pressure? Who is in charge of navigation / SMB deployment / safety stops? All these are discussed before we even hit the water.
Big, big difference in how training is conducted across different agencies. From what I learned talking to GUE instructors, Fundies is even more stringent, and requirements even higher.