It has to do with managing resources.
The DEA has a set budget. They could spend the bulk of that money arresting individual users in states that have legalized marijuana (both medically and recreationally) then spend even more money during the trials, and even more when the states sue the federal government (it's going to happen soon) because the constitution guarantees that states can decide on their own regarding any issue not specified in the constitution (that includes the prohibition of a substance, like marijuana and alcohol).
Or they could allow the states to manage their own affairs and direct those funds towards interstate sales and trafficking, large scale illegal growers and harder substances. What do you think is a smarter use of funds? Going after John doe, the guy who smokes a joint or two a week, or going after illegal grow operations in the middle of our national parks that were set up by illegal immigrants?
Curious cat brought up an interesting argument. Illegal immigration is in the same boat. Obama came out and stated that he would direct ICE to focus less on illegals who came here as children and were law abiding. This doesn't mean he stopped arresting illegals, in fact he's deported more than Bush and Clinton combined. What it does mean is he realizes that he could waste money going after illegals who have lived here their entire lives or he could wisely use the money to go after illegals who commit crimes, who bring other illegals across the border, or the businesses that continue to hire them. It's a question of what we can afford to do and what has the best value.
Arresting individuals who aren't harming others is just a waste of money and everybody knows it.