My personal opinion:
1. Removing a ton of important features from a plugin is crippling the plugin. One guess for why a plugin developer might claim that it isn't is because he figured it'd be the best way to make money and he would like it to have no downsides. Cognitive dissonance is an amazing feature of human brain that causes our thinking do this: "I made a choice", combined with "I value my capability for rational thought" so "that choice must be great".
The downside of cognitive dissonance is that it disables our ability to learn from mistakes.
Learning to resist cognitive dissonance is one of the most important steps in learning to learn. If you want to make money, you need to learn to make money, and to be most effective in learning, you must learn to learn. If you want to achieve anything, you'll benefit greatly from resisting cognitive dissonance.
2. Based on the feedback here and in http://wordpress.org/support/topic/what-a-kick-in-the-teeth, it seems that it would have been far better to leave the features to the back-end code of the free version, add notes to UI that certain features will be removed or restricted in the future, and when it's time for that, remove the features from UI only, so the update won't break any existing ad configurations.
3. Showing respect to others, their feelings and opinions gets you both respect and money in return. It can take thousands of hours to make a good, comprehensive plugin like this. Showing appreciation to users' points of view - especially when they are seemingly in conflict with the plugin author's own views - takes a couple of minutes a day and can more than double the long-term income.
Instead of driving people away it's better to treat them exceptionally respectfully, so that they will be your brand ambassadors, converting their friends to your future customers.
4. After you've done something that customers feel is wrong, you earn a lot of love with a single "sorry". And instead of "no" it's a good habit to say "yes, but". The purpose of that "yes" is to validate the other's feelings and concerns. For example: "I understand your concern. The reason I have planned on removing those features is: ... Thank you for understanding my situation. Comments are warmly welcome."
Comparing my own human interactions before and after the learning of these feels like I possess now super powers that my previous self would have found so amazing they're borderline unreal. This part of personal development comes a bit by bit. I recommend every step of it.