Since my day-job involves designing game-mechanics (video games), I'd like to weigh in on this one by looking at the main purpose of those three metamagic feats and the issues they are (probably) meant to counter.
Still spell allows a mage to cast a spell when they are unable to move their arms or body, such as when tied up or buried up to their neck in sand. This seems to be the primary purpose of the feat.
Silent spell allows a mage to cast when they cannot speak, such as when they are silenced or gagged. In many cases, they may also be unable to move their body (such as Hold Person or bound and gagged) and need both of these feats. This seems to be the primary purpose of the feat.
Eschew materials allows a mage to cast when they don't have access to their normal (cheap) spell-materials. Stuck in a prison cell, they are likely to need this feat. When they have emptied their spell-component pouches, they will need this feat. This is the purpose of the feat.
As to using all three together... Anyone who thought to bind and gag a mage probably knows enough to take away their spell-component pouches too. This makes a perfectly-normal case for using all three together.
Since there are strong justifications for using the three feats together and in pairs, I don't see that 'stealth casting' adds anything to the game except unbalancing the counter-spell rules.
Also, I second the idea that there will be other visible signs of spell-casting going on; magic in pathfinder is tearing at the walls of reality to create effects which break the normal laws of physics, so glowing lights, strange smells and odd noises would be quite likely.
Finally, the rules say nothing about any of these feats making a spellcraft check harder. Normally, the rules will tell you if a certain mechanic affects another one in this way - look at how they explicitly tell you that you cannot hide while holding an uncovered light-source, even though it should be obvious - and so I would rule that the feats are designed to allow spell-casting under difficult circumstances, not to make it invisible. That is, until we get some errata from the development team...