Chris, I favor a combination of letting nature take her corse and introducing other native species. Basically, you should learn how to identify problem species, and eliminate them as you find them (sometimes easier said than done). By eliminating the invasive species, you will increase the potential for beneficial species to establish themselves & spread. Having said that, if there are no Arrowheads within miles of your house, don't expect them to pop up. Instead, introduce a moderate amount of several species of beneficial aquatic plants, and see which ones do well. It may happen that some die off and others take off.
As for which species, the same ones talked about above are fine...some may be better suited to different habitats than others...read individual descriptions from wherever you purchase them, or ask the supplier. The only difference with larger bodies of water is that they are more likely to be able to support beds of cattails or other invasive native plants without them becoming a major problem. However, I have seen plants like Phragmites (Common or Giant Reed) surround 5-6 acre ponds, creating an undesireable monoculture.
