Edit: Responding to JGulik, not abyssaldeath.
Yeah. As I'm sure you're aware, the issue isn't merely that it accelerates the process -- it's that the chance of a best-case final outcome doesn't actually improve at all.
For save-ends effects with no penalty on failure, extra saves are nifty. As written, for situations where fails are bad, they're pretty much value-neutral. As soon as I became aware of the implications of extra saves on things like petrification, I immediately decided my houserule was required, and I wouldn't be surprised if it was intended to work like that, even though the text of the rules offers no actual support for such a ruling.
@abbysaldeath: The halfling feat in your example can be relied upon to provide better or equivalent results almost every time. The odds of a worse result don't outweigh, or even equal, the odds of a better or equivalent one. The only reason (based on the odds) not to use it is because you think it might be more useful later.
OTOH, with extra saves vs progressively worse effects, you're making a decision to live/die quickly or live/die at the normal rate. But you don't effect the chances of living or dying at all. If you're happy with that, cool. It doesn't sit right with me, though.
Essentially, using Second Chance might hurt you, but it reliably increases your odds of surviving the fight. Using a bonus save on the sorts of effects we're discussing has zero net effect on your odds of survival.