@ScytheX I'm not at all against a plugin being created for this purpose. I agree with you that it would be far more efficient to have a plugin that can do this quicker, tidier and even easier, like you are saying, however if there is currently no plugin that does it, this is a better method than nothing.
For me though, at first glance I would think this method is hardly any extra effort once I know what I'm doing. I can leave enough gaps between skills in the database and make each upgrade directly under the next to prevent them becoming messy or confusing in the database, then the notetags
@Zarsla gave makes it even easier to just copy and paste them into the right skills changing skill ID's quickly.
For me, from looking at it at first glance, it's not that much extra effort with this provided solution. I can say that confidently because in the past when I had to do something similar for RPG Maker VX but with events that was much more confusing then this, it wasn't too much effort for me, and that was way more complex then this solution provided here. This was when it very first came out.
As long as you know what you are doing and plan your skills ahead of time it should be ok. Leaving enough gaps in the database will make it easy to change and add upgraded skills later if you need to. That's the only part that require some thought ahead of time, I think.
But, at the same time, it sounds like this solution is not easy for some other people, I guess?
The plugin has been requested here and is still a open request, so perhaps someone will make that plugin sometime soon.
If OP has left or doesn't request the plugin anymore, you can always request one.