Well, it has been a
long time since I played 3E with only three saves, so I was literally digging out my player's handbook and reviewing them because suddenly I realized there are really only two save types:
1. Avoidance (Reflex)
2. Resistance (Fort and Will, each in their own fashion)
I came to this when I was thinking how I would distribute the strong and weak saves in 5E, because if I paired ability scores down into 3 saves, I would want a strong and weak represented in each pair. To recap:
Strong saves are: DEX, CON, WIS
Weak saves are: STR, INT, CHA
So, while your "initial concept" paired CON and WIS to create FORT (a logical combination), it merges two strong saves into one.
My "first draft" would be to do these combinations
FORT (CON, CHA)
REFLEX (DEX, INT)
WILL (STR, WIS)
These combinations merge a strong and a weak, as well as a mental and a physical, into the three saves.
Finally, each class would gain a "full" save and a "half" save (use half proficiency, round down) and would use the
lower ability score modifier from the pair (I am a tough DM

) instead of the higher score modifier.
A feat such as Resilient would provide a +1 ASI and a "half" save. You could combine the half save with the one the character already has (thus, gaining two full saves) or apply it to your remaining save (thus, having one full save and the other two both half saves).
If a class feature gives proficiency in a saving throw, you get a half save in whichever the normal ability score falls under. If you already have half proficiency, it becomes full. If you have full already, you can choose to give half to a different save.
The classes would be (FULL save, HALF save):
Barbarian (FORT, WILL)
Bard (REFLEX, FORT)
Cleric (WILL, FORT)
Druid (WILL, REFLEX)
Fighter (FORT, REFLEX
or WILL)
Monk (REFLEX, WILL)
Paladin (FORT, WILL)
Ranger (REFLEX, WILL)
Rogue (REFLEX, FORT)
Sorcerer (FORT, REFLEX)
Warlock (WILL, FORT)
Wizard (WILL, REFLEX)
If you default the Fighter to FORT, REFLEX, you might also notice each save is represented four times as the full save and four times as the half save throughout the classes.

(I am OCD and a Libra, I love this stuff!

)