By regenerating eroded and degraded water ways this not only creates water retention but it also creates some drier micro-climates. If you look at the plans for
Sepp's Project in Kasakhstan, while on a much bigger scale this sounds like a similar situation as yours. Too much water in the wet season and too little in the dry season. Regenerating landscapes is about balancing and buffering these extremes, to provide better growing conditions year round. When removing the sediment from these soggy areas and enlarging the water retention you are often creating hugelkultur (smaller scale) or berms (larger scale) with this sediment.
Having retention landscapes for the water to stay relieves the pooling and root rot problems in your current growing areas. The stored water slowly wicks into the landscape over time, providing moisture to the trees when they most need it. This is a big part of why Sepp is so against liners, they don't allow the water to wick into the landscape. In turn the water becomes stale and now you have a maintenance nightmare.
The spillway you create determines the level that the water can flood during the wet season. The flood zone provides the buffer space between the wet season and dry season, and ecologically functions like a wetlands (a tremendously productive ecosystem). Water is the most productive growing medium, if your trying to create the most productive ecosystem you can, in my opinion there is no such thing as too much water.
Deep rooted and de-compaction plantings can certainly help water seep into the soil. In addition to alfalfa and clumping grasses try turnips, radishes, and the like to help break up the soil. These also provide excellent forage for both humans and wildlife. While this might help a little, I don't think it would solve the root of your problem.
I think Sepp's strong opinion on water actually comes from how much he has traveled the world. All over the world people have problems with flooding, followed by problems with drought. The climate is not the issue, it is our management of the landscape.
In a resilient ecosystem there is enough diversity to accommodate the extremes in climate. For example in a wet year like your last summer John, the Krameterhof would have bumper crops of mushrooms, water plants, crayfish, and fish. Granted the cherries are all going to split, but there is enough diversity in the system to accommodate these natural fluctuations. In a horrible drought (like they had last summer) there aren't going to be any mushrooms but the cherries and pears will be of the highest quality. Their strategy is to have enough diversity that every year, no matter the conditions, there is a bumper crop of something. They don't worry about the crops that are stressed, instead putting their energy into harvesting their bumper crop. It is really a brilliant system, grow an incredible diversity of crops and only harvest the ones that do best in a given year.