Well, it's less of a "This idea is stupid!" and more a "Game design is complicated and this is why they can't exactly just put in effects like this easily."
You're right in that they COULD implement things like this into a vertical progression system. A lot of the cons that I mentioned only crop up if gear doesn't get replaced, that's what causes newer gear to be invalid upon release and leads to horizontal progression schemes that require low drop rates to keep people still doing content. The problem is that when you add in ability augments the balancing becomes MUCH more difficult to do, especially since you may need to not only balance the new gear coming out to ensure it's an improvement over the lower level gear, you ALSO need to keep an eye on balancing low level gear that may have some unforeseen synergy with newer equipment. Adding in such a system not only makes items harder to balance on an individual level, but also increase how many items they need to balance at a given time. I know when the difficulty of balancing has been brought up before, people tend to say "Well just do your damn jobs and work on it SE!" I don't think they're quite grasping how much harder it is. And the unfortunate downside is if they fail to balance it properly, it leads to all those downsides I've mentioned before.
Now, as far as the ability sharing in the FFIX system idea, a thought did occur to me. Considering that these abilities would come off of gear, an easy solution would be to have each ability still tied to the slot that piece occupies, and only be able to equip one piece per slot. So, in this sort of system, if the +20% speed on crit and spear cannon swap both come from weapons, then they wouldn't be able to both be used at once.
As an aside, I actually really enjoy debating about this kind of stuff. Game design fascinates me. However, I also understand that development time can be a limited resource and game design can often be an ungodly mess even before adding in additional features. So, I tend to err on the side of solutions that are easier to implement, and try to help my fellow players understand why certain much asked for features might not get implemented very soon.