The smaller heaters are slower to heat, and will operate more often to keep up with the output of larger heaters.
Larger heaters are a small bit more efficient than the smaller pool heat units.
Ask yourself a question about your anticipated usage patterns. If you will be heating intermittantly, for example, turning on the heater on Friday, and turning it off on Monday, then a quick heat up is required. Heaters only add 1-3 degrees of heat per hour to the average pool. A larger heater is best for this usage pattern. If you expect to be maintaining a temperature by setting the thermostat, and maybe adding a few degrees in the evening or on weekends, then a smaller sizes of pool heaters can be used.