Take away with the left hand but give with the right. If you just take away these skill functions, the players will gripe. If you say 'I want to replace these very nebulous skill functions with very specific things that are easier to adjudicate so we don't get into cowboys and indians territory' then its easier to swallow. Especially if it lets them get mechanical bonuses they couldn't otherwise have.

For example, you cannot tell 'everything' about an existing spell effect by making a Spellcraft check, but what you can do is give the party a +4 Insight bonus on saves against that effect when someone triggers it. Or get a +4 bonus on CL checks to dispel it.

You cannot tell everything about a monster by making a Knowledge check, but you can decrease its DR with respect to your attacks by 5 points if you hit the usual DC, or 10 points if you beat it by 20. Or (not and) you can decrease its elemental resistance for a specific energy type with respect to your attacks by the same amount.

Or how about this - as a Swift action, make a Knowledge check about a monster with respect to one specific spell/skill/ability/attack. If you succeed, you know whether the monster would: Be particularly vulnerable (as in take more damage or a penalty to saves, not tactical sense), have no particular resistance or vulnerability, be resistant to it, or be immune to it.

The new things are still nice for the players, and they also interfere a lot less with your ability to have things be mysterious or make the players figure things out.