Reflex: Strength & Dexterity
• Strength (big athletic body movements)
• Dexterity (small sensitive movements)
I'll buy Strength in Reflex. It might work well in Fortitude as well though.
Fortitude: Constitution & Charisma
• Constitution (physical toughness, immune system, persevering against exhaustion)
• Charisma (luck, innate magic, fate - in D&D 1e Gygax defines these as nonphysical hp)
Referencing 1e and Gygax just seems to be a handwavy way of justifying Charisma here rather than Will (portraying Charisma as force of personality, sense of self, and confidence). It's a very odd fit. Since Cha isn't used for anything related to health (hit points, tests of endurance, etc) it seems a stretch.
Will: Intelligence & Wisdom
• Intelligence (knowledgeability, analytic search, reason)
• Wisdom (sensory perception, instinctive willpower)
Intelligence kinda fits...
The problem with this schema, like in 4e, was that you have two physical saves for three stats and one mental save for three stats. So there always needs to be a mental stat in a physical save. Which is awkward. And there's the effort for forced synergy to have each stat in one save, and each save have two possible ability scores. Which matches, but doesn't always make sense.
Symetry might not be the best way.
If sticking with the three, having Str or Con for Fortitude make sense; Str or Dex for Reflex is good; and just accept the unevenness and have Int, Wis, or Cha for Will. Maybe tack on a rider that the same stat cannot be used twice so you cannot have Str for both Fort and Ref. But this is complicated, as every time you tack on a rider like that you're adding a point of failure that someone might miss and make a broken character.
There's also no strong reason to have three saves beyond "that's how 3e/4e did it". You could have four with a floating option in each (again, risking errors), adding another mental save (Personality? Sense of self). Or you could just combine Reflex and Fortitude and have "Physical" and "Mental" Saves.