@xzesstence - There's a lot to unpack but hopefully this will help you see it from our position.
First off we care extremely about our existing customers - this is why we spend so much time on support and maintaining our assets. By releasing a version 3 it shows that we are still committed to our customers while also still having it make business sense. I know that you don't have the numbers in front of you, but so far the uptake of version 3 has been going really well. In fact the main character controller is number 2 in popularity on the Asset Store right now:
Will we in the future change the upgrade percent to 75%? Maybe, but right now we are happy with the conversion rate and overall have received positive feedback on version 3 so we not going to at this time. That definitely doesn't mean we won't change it in the future though. In deciding the 50% we used the data from the version 1 to 2 upgrade four years ago and also talked to existing publishers who do paid upgrades.
I definitely feel for your situation, but at the same time version 2 is still a great character controller and it is still supported. We may extend the support for version 2 past the end of the year depending on how quickly everyone converts, but at this point the rate of upgrades is going well so we'll see. It also still makes a lot of sense to use version 2. I haven't finished any of the version 3 integrations or add-ons. Version 2 is also really stable. We did a lot of testing but things like the new locomotion system and modular item system in version 3 will likely take some time for the dust to settle.
In the version 1 to 2 upgrade we had a grace period of 30 days. This was one of the areas that we used the feedback received from the previous upgrade cycle to determine 90 days. 90 days is also the upper range of what Unity recommends:
Would I like to be able to do a scaled upgrade price where those who purchased 4 years ago have a higher upgrade than those who purchased 91 days ago? Absolutely. I think that would also help with the conversion rate and make everyone happy about the upgrade. It hurts me seeing the complaints about the upgrade, but I also know from a business perspective we need to do it.
I hope that helps you understand the reasoning for the upgrades and why they are what they are. I am glad that you were able to get the downloads working.