These are only my opinions. I am not a trained hydrographer nor a naturalist. I read a lot, and I have observed the Flats during most of my life. I have played and experimented with water flowing through soft ground until I think I understand somewhat about the ways that it behaves. I've asked older members of my family, neighbors, and complete strangers about "the way it was back then."
Deltas and marshes evolve. Come back in a century or two and you might not recognize the place. At all times the water is dropping sand and silt in one place while it is carrying it away in another. There is constant struggle between the flowing water and the land. The land has its allies: vegetation (particularly willows), and more recently, man, with his sea-walls and notions about shoreline property. Flowing water has time and the almost boundless energy of a planetary weather system.
In the Flats, most of the deposition takes place where the current is slowed by vegetation and shallow water. The erosion is concentrated in and near the channels. These effects are modified by changes in the overall level of the Great Lakes system.
When the water is low, these effects are exaggerated. Shallower water means less water flowing directly out of the main channels through the marshes. The water must go somewhere, so it rushes through the smaller channels, scouring them out. The slow water in the marshes has time to drop more of its load of sand and silt.
When the water is high, the opposite happens: water easily flows through the deeper marshes, sometimes fast enough to carry away some silt. The water, with other places to escape, is flowing slowly in the little cuts and channels, allowing sand and silt to be deposited which gradually fills in the channels, which in turn sends more water through the marshes.
Historically, the water level changed in cycles -- seasonal ones, and longer ones of years and tens of years. Recently (about 30 years) the water seems to have remained quite high for longer than usual. The sharp drops in level that leave parts of the marshes nearly dry and scour out the little channels haven't occurred for a long time. Check out the Army Corp of Engineers Historic Hydrographic Data.
The marshes, too, need changes in level. If the water stays at the same level for long periods there is loss of diversity. In a given depth of water, one kind of vegetation will take over; in another depth, another vegetation will prevail. When the water keeps changing level, no single type of vegetation can take over an area completely. Mono-cropping is bad practice for farmers; nature doesn't normally do it either.
I haven't seen some varieties of plant out here for years. They used to be common; in one place one year, another place in another year. Some plants thrive on change: their competitive edge is that they can come back faster than other plants when conditions change to suit them. Stable conditions extinguish these plants.
The things that stable water levels ARE good for are shipping interests and shoreline property values. We need to be sure that the health of the marshes are taken into consideration as well, if any plans are advanced to control water levels.
A little investigation shows that Niagra Falls acts as a self-regulating spillway and controls the levels of the middle lakes, so this long stretch of high water is due to an abnormally long series of high-precipitation/low-evaporation years. Most people I know have simply raised their docks and seawalls to match these high levels. What they plan to do when water levels go back down, I don't know.