No major difference in overall safety, but generally speaking much easier to regularly test GFCI receptacles for the average consumer, than breakers. You simply push the test button, or use one of the plug-in style testers sold at most hardware stores.
http://www.kleintools.com/catalog/electrical-testers/gfci-receptacle-tester-usa-made
Also, if ALL circuits are protected by GFCI breakers, then the entire circuit would trip off every time a slight variance in current was sensed, that could include ones lights. Not a great idea, especially when it's past sundown.
Much better to simply protect those areas that require protection, where water is located, such as kitchens, bathrooms, receptacles located outdoors, fish rooms, etc.
I believe that the current building code in Canada requires that any receptacle within 1 meter of a damp location (sink, tub, etc) requires GFCI protection.
Also of note... I was referencing power station early design variants and not modern highly sensitive designs.
I was referencing what the average hobbyist has available to them, which in this scenario is all that really matters. GFCI's have been used for decades, and in both residential and commercial applications have been saving lives for decades.
A grounding probe/GFCI combination is pretty much the safest way to protect one from electrical shock when working around tanks full of water, that are attached to lighting systems, power heads, filters, heaters, etc.