Using resources to counter or mitigate is another question. You bring up a good point in that the high-level party with a Paladin (whom everyone sticks close enough to) or with casters who learn/prep & use the right spells at the right time will have a lot of resources to make up for bad saves - or for other purposes, high-level full casters are very versatile that way.
Or any of a number of other mitigations. Even something as simple as taking the Lucky feat is akin to universal proficiency in All Important Saves, if you use it that way. Then there's elvish advantage against charm and Berserkers' and some Paladins' immunity to charm, Fiendlock's Dark One's Whatsitcalled (AFB), Evasion (effectively an auto-success on many Dex saves, with a chance at uber-success), Tides of Chaos... the list goes on and on.
Some of these cost resources, others don't, but even if it does cost resources it doesn't make sense to exclude these features from analysis unless you're analyzing utterly trivial saves, like the chance of failing your DC 10 Dex check to slip on some ball bearings during the last round of combat. If you explicitly limit your analysis to trivial saves then sure, no one would ever* use Bardic Inspiration to avoid falling prone if the only consequence is not being the one to strike the killing blow against the last monster in a random encounter. But if we're talking about saving throws against important things, like being banished to temporal stasis for five thousand years (as mentioned in this thread), these things are very relevant. Even if it's just a question of "do you take 20d6 poison damage from the trap or save for half," these mitigators are important. A 12th level Cha 20 Con 14 Paladin may not have proficiency in Con saves, but he can
still take
12d6 (42) (Con save DC 19 for half) purple worm poison damage and make the DC 19 Con save 45% of the time (
32.55 average damage), and he can make the save 70% of the time and cut the damage to 13.65 on average just by casting a little Protection From Poison spell on himself (no concentration, 1 hour). That's
better than having Con save proficiency.
* And yes, I realize that by saying "no one would ever...", I guarantee that I will very shortly see some player do exactly this thing during play.
Saving throw proficiency is not your first line of defense. Never has been**, never should be.
** Except maybe in 3E or 4E, about which I know little.