Time and again folks have pointed out to me that an armored up Synthesist does not use the Eidelon's saving throws. Where is this stated? People have simply said that it is inferred by omission.
Okay, so if that's true, does the Synthesist use the Eidelon's ability modifiers? What if the Eidelon's ability is below the Summoner's? Constitution jumps out at me as the obvious one here. It seems strange that a hearty Summoner (say, a Gnome) takes a hit to a Fort save while in the Synthesist skin.
Not using the Eidelon's saves AND being stuck with a potentially lower stat seems like the worst of both worlds. I wish there was an FAQ ruling on this, like there is for the the BAB question.
The summoner is the character so his saving throw is used, but when they are combined with the eidolon he uses the new fort save modifier for con. The only way the eidolon's base saves could be used in place of the actual character is if the rules allowed it as an exception.