The only plants that are in pots are the water lilies because they need to be protected from the koi rooting them up. All the marginal plants are set directly in the gravel so their roots are free to run & soak up the nutrients which helps keep the algae at bay. My favorite plants are.... well, ALL of them!!
I have lots of different iris, red-stemmed parrots feather, water celery, arrow plant, bog bean, ribbon grass, blue pickerel rush, several pitcher plants, turtlehead, variegated sweetflag, corkscrew rush, lizard tail, and... I'm probably forgetting someone. I do have some non-hardy plants in there too - impatiens, water hyacinth & umbrella palm (the latter is overwintered indoors, the others are replaced in the spring) I have one shelf area that needs a bit of a re-do next Spring, so I'm probably going to be looking for something different to try as well. (yes, I'm a plantaholic & could probably use with an intervention!)
How long have your ponds been up & running? I absolutely LOVE the 'floating' stepping stones across the middle. Your flagstone bottom will probably get a little slippery, so be careful walking on it once it gets a bit of an algae coating.
I'm sorry about your heron problem - We (knocking frantically on wood right now) really don't have them in our immediate area. I think the heavily wooded location keeps us a bit hidden from sight. I know that netting the pond is pretty much the only way to really foil their attempts to help themselves to your fish. Lots of good ideas on this forum from others that have rigged up net systems. I do occasionally lose a fish to raccoons, but fortunately not too often. They go more for the frogs, which we have a lot of.