Hey it's been a while since I checked here, so I apologize it's been so long to respond.
I think you're right, and the two can be combined. I'd simply increase the role Willpower plays in Resilience since most of the physical is represented by Toughness.
Toughness (Endurance MV ×2)
Resilience (Endurance MV + Willpower x2 MV).
I've been tempted to make Resilience work only against non-physical magic and psychogenic attacks, and rename the DP (Defense Pool) Resistance instead. In other words, move Resistance from being an Ability and make it replace the broader "Resilience" Defense Pool.
Toughness (Endurance MV x2)
Resistance (Willpower x2 + other relevant specializations or masteries)
In my quest to create a game that fits me and my gaming-style perfectly I keep pounding away at Eldritch. Recently Endurance and Resistance caught my attention due to the fact that they are very very similar. Even so that a roll to resist poison or enviromental/climate could be either one of them. My kneejerk reaction was to just lump them together and be done with it. One of my players pointed out it would open up for a fair bit of min-maxing if that Ability would be the basis for both Resilience AND Toughness.
So now I'm at a point where I don't like the fact these two Abilities are separated since they are so similar and I have a hard time as a GM to make the call whether or not a roll should be for Endurance or Resistance. I still don't have a good way to solve Resilience and Thoughness though. I could make them both a bit weaker and let Resilience be Willpower x2 and Toughness be [Resistance/Endurance] x2.
Anyone have any suggestions on how I can make a good change here? Add a static value to Resilience and Toughness + relevant Ability? Add some other Ability to Resilience/Toughness beside Willpower and [Resistance/Endurance]? Some other approach all together?