First, let me explain the context of your question: It is about a concept for a future airliner:
Boeing Blended-Wing-Body Model 450-1U, taken from NASA/CR-2006-214534.
In the artist impression above the engines are podded and sit on struts in order to achieve a uniform flow field at the intake face. However, the strut and nacelle surface area will contribute drag that could be avoided if the engines would be mounted closer to the rear fuselage. The picture below, taken from the same source, shows a CAD rendering of a possible geometry with semi-buried engines:
The disadvantage of this concept is the ingestion of boundary layer flow such that the speed profile over the intake face shows a speed gradient (BMI = boundary layer ingestion). This will result in distorted flow at the compressor and cyclic pressure variations for the compressor blades, which in turn will require a more robust and less optimized compressor geometry or run the risk of compressor stalls and early blade failure. Also, the energy loss within the boundary layer results in lower pressure recovery ahead of and inside the intake, which will increase specific fuel consumption.
Or to quote the NASA page on inlets:
As the air is brought from free stream to the compressor face, the flow may be distorted by the inlet. At the compressor face, one portion of the flow may have a higher velocity or higher pressure than another portion. The flow may be swirling, or some section of the boundary layer may be thicker than another section because of the inlet shape. The rotor blades of the compressor move in circles around the central shaft. As the blades encounter distorted inlet flow, the flow conditions around the blade change very quickly. The changing flow conditions can cause flow separation in the compressor, a compressor stall, and can cause structural problems for the compressor blades. A good inlet must produce high pressure recovery, low spillage drag, and low distortion.
The question now is: What can be done to keep the semi-buried engine concept but to avoid the intake flow distortion from boundary layer ingestion?
As it turns out, the same NASA paper proposes a simple diverter ahead of the engines which is supposed to push the slow boundary layer to the side:
An even better solution is to use a splitter plate; after all, the semi-buried engine has an intake very similar to the side-mounted intakes of trainer and combat aircraft. Below is an example from another subsonic aircraft, the Czech L-39 Albatros jet trainer:
Subsonic splitter plate intake on the L 39 (picture source)
Less commonly used, boundary layer suction can be employed to remove the slow-moving air close to the surface and to re-establish a more uniform speed profile. Here my example is the Eurofighter EF-2000 intake, where boundary layer suction is used to remove the boundary layer that has accumulated on the splitter plate itself:
EF-2000 intake, here abused as a baggage compartment. The grid of holes is used to suck away the boundary layer.
A similar arrangement was used on the intake cone of the SR-71, but I did not find a good picture. Boundary layer suction, however, is not the kind of passive solution you desire. But it has the advantage of being adaptable to the specific flight situation.
Also not passive, and not being used in existing airplanes, would be a moving surface ahead of the inlet. This has been tried with rotating cylinders at flap breaks, and there is some literature covering the topic. The moving surface will reverse the effect of the wing ahead of the intake and re-energize the boundary layer right ahead of or inside the intake.
In all cases, you need to check whether the newly incurred losses of the boundary layer manipulation will be lower than the gains in engine efficiency. I did not go into vortex generators: They might help to equalise the speed loss or at least to reduce the speed gradient towards the surface, but they incur new and intense losses all by themselves and would most likely reduce efficiency a lot. If well placed, they will reduce intake distortion, but at the price of a much reduced pressure recovery.