This code rewrite is really welcomed. The product is good but code is far from being easy to extend because of the way it was built.
The functions API could make extending MainWP a lot more powerful. Getting a list of websites in an extendable table should be an easy task. Many of your plugins don’t use the same way of getting sites that is used in the main plugin.
The reports (Pro and HTML) should have the UX/UI rethink too. It’s too easy to send all reports by pressing when you wanted, instead, to search within your sites list. Not sending reports that created an error is a must. Knowing what was sent and when would be great.
All this to say that a code rewrite is great thing… but it is not only about recoding, it should be also about revisiting the UI to fix all these small things that make management difficult at some point.
Please see all this as a positive and constructive review. We want to continue using the product and want it to be better!