For starters, let's examine things in the context of terrestrial reserves, because some of the interesting issues of marine reserves that I will get into later in this post do not necessarily apply in a terrestrial context. Let's say you have the budget to protect 100,000 km2 of land. Is it better to have a single 100,000 km2 preserve? What about 10 10,000 km2 reserves? 100 1,000 km2 reserves? Some other optimal size?
The first step in determining this is having a clear goal of what you want your reserve to be able to do. Are you looking to protect a particular species? Is there some landscape feature you want to make sure will remain for future generations to enjoy? Are you trying to retain Ecosystem Services (this is a term that refers to what ecosystems can do for people--think of things along the lines of marshes in the Gulf of Mexico buffering against storm surges)? All of these will require different reserve designs.
In a marine environment, things change even more. One of the key differences is that, if you put something in a terrestrial environment, you can expect it to stay where you put it. In a marine environment, this is far from the case. While there certainly are marine environments worthy of protection that are static--reefs, seamounts, kelp forests, et cetera, in the open ocean things are far more dynamic. Resources can move around on currents, and predators can follow prey species great distances looking for dense patches that may last only brief times.
What this means is that, in a marine context, you need to do one of two things: either have truly gigantic reserves so that, by the law of averages, the stuff you're trying to protect will be within the reserve most of the time. The other option, and the road often taken is to, rather than trying to protect a particular area, restrict activities that might otherwise have detrimental effects on conservation targets. This may range from fisheries regulations--seasons, catch limits by biomass, and equipment restrictions, to dumping restrictions and everything in between.
That being said, I am in no way, shape, or form trying to criticize the President's actions. Marine reserves do work. Repeated studies have shown dramatically increased biomass within reserves, and even outside reserves but near their borders. They are so successful that fishing vessels often loiter near the borders of reserves due to increased fish biomass. The point here is that, when it comes to conservation, there are more complex concerns than "protect everything everywhere and that'll be fine".
Papers for consideration:
Halpern, Benjamin S. 2003. The Impact of Marine Reserves: Do Reserves Work and Does Reserve Size Matter? Ecological Applications
W. F. Humphreys and D. J. Kitchener. 1982.The Effect of Habitat Utilization on Species-Area Curves: Implications for Optimal Reserve Area
Journal of Biogeography