Water movement is the key. Each species has an ideal water flow and alternating currents best match the variety of needs that these different corals have. Also, alternating currents tend to stir up detritis better than fixed flow. So while alternating currents will best reproduce natural reef flow, the key is to keep the flow high, indirect (not blasting the coral), and observe how each coral is responding. Try to learn about where your particular species grows in the wild ( for example: reef flat, outer margin, or lagoon) or where the previous fragger grew his/her colony and try to match that environment.
The biggest problem reefers experience once a reef is established regardless of current styles ( fixed, alternating and surge) is keeping the flow up as the reef grows and matures. The increasing growth of corals slows the water flow down. You might say it's not a problem I would mind having, but for those experiencing the problem will tell you it presents quite a problem. The only quick fix is to frag out the corals.
The biggest problem I have run into with alternating current devices is that they either don't look good in the tank (power heads), cost too much and or are not reliable. Unforunately these mechanical devices don't always stand the test of time and elements. If you can afford them, don't mind their appearance in the tank and do any required maintenance, then alternating is the best way to go!