To be perfectly clear, I do not think this was a missed opportunity.
I this it is. The 3-saves system isn't bad, in fact it worked ok in 3e, but I was hoping for something better and for a progressive idea. Actually, they had the idea since the start, talked about it many times, but never pulled through with it until they finally went backwards. But they didn't pulled through the other way either since as you say we get also the other 3 useless saves in the game.
I wish they held on to their first idea that saving throws could be nothing more than ability checks, hence working towards the general emphasis on the 6 scores in 5e. I liked the first implementation when we didn't even have a level-based bonus to ST (and spells DC). But then instead of going forward and completing the idea, they went backwards to 3e saves (without the floor value).
I would have preferred more representation of Int, Str and Cha saves in spells. If they wanted to,
it would have been easy to do so: they could have picked all paralyzation-type spells and gave them a Strength save, all illusions and give them an Int save, and all compulsions/charms and give them a Cha save (representing a challenge of personality between the caster and the target). It would not be important to really achieve an even spread (i.e. ~15% spells each save) but at least a significant representation of all 6.
It would have helped a bit with the long-time problem of dumping stats. Almost nobody dumps Constitution (at least because of the HP), and only occasional PCs are given low Dex and Wis. Why? Because those 3 abilities are generally perceived as
defensive abilities, something you're going to pay for if you have it too low,
because you cannot choose when to use them: you'll be hit more often with a low Dex (however now in 5e we will have heavy-armor wearers dump Dex more easily) and you'll be attacked by surprise more often with a low Wis.
Strength, Intelligence and Charisma are
proactive abilities i.e.
you choose when to use them, and that actually means that you can always choose just not to bother with that strategy: you have a low Strength? Fine, you just don't use melee weapons, you use spells or ranged weapons; you have a low Intelligence? You just don't play the sage/knowledged guy; you have a low Charisma? You just let someone else speak for you. *
These three stats get dumped all the time, and the 6-saves system at least gave me some hope of mitigating that.
* remember that you have to see these the other way around, because it's not that you just happen to have a low Strength
therefore you choose not to use melee weapons; the reality is that if you've decided to be a spellcaster or archer
therefore you can afford to dump Strength at no cost, while nobody can dump Con/Dex/Wis at no cost