The panel on the right is too complicated. Let's logically group them (save/load related, topology change related, layout options, layouts, etc.) and put them under accordions.
Let's make sure all buttons are consistently named using plain English: "Tick Delay" vs "swapForceLimit" vs "Add Nodes to hiearchy randomly"
Swap check boxes and their labels (first the checkbox and then the label).
Let's organize the following by:
Let's have two section: Samples and Experiments. Experiments should have all the experiments we have right now. Samples should have samples like the one we have but when we select them they should load with nodes already pre-determined to be in the hierarchy. Here we should add 4-5 more sample where the hierarchical part is like the ones we always imagined (tall and not very wide).