The original poster's point is well taken.
"Identify a spell being cast. (You must see or hear the spell’s verbal or somatic components.)"
"A character faced with proof that an illusion isn’t real needs no saving throw."
NPC Wizard casts an Illusionary Wall.
PC Cleric only has to hear him doing that, or see him doing that. So, even if the Wizard is invisible, it is a little tougher to pull this off (and yes, he could make it Silent as well, but that takes a feat and a higher level spell and special spell prep for most Wizards).
PC Cleric states that it is an illusion and swings his mace through it. All of the rest of the PCs automatically save.
Plus, there are usually multiple PCs that have SpellCraft in many groups, so the chances of pulling off an in-combat illusion is even less.
The bottom line is that SpellCraft tends to often invalidate in-combat illusions. A skill that is more potent than a significant portion of an entire school of spells. Hmmmm.
I think the only way around this is to have the NPC Wizard not cast Illusion spells in combat too often. Illusions would become the domain of out of combat, long range, under special prep, etc.
An interesting house rule would be to have opposed SpellCraft rolls (the caster of the spell has to use up a move action to accomplish this) in order to fake out opposing spell casters from knowing what the real spell is. If he wins the opposed roll and his opponents make a normal SpellCraft check, they think he cast a real Wall of Stone as opposed to the Illusionary one. If he loses the roll and his opponents make a normal SpellCraft check, they think he cast an Illusionary Wall of Stone.
Btw, in my game, characters have to make a Listen roll for any spell cast beyond 30 feet in combat (or other noisy conditions) and beyond 60 feet in relatively quiet conditions unless they can clearly see the caster. If they can see him, they can make a Spot roll beyond 30 feet instead (or both rolls is they can both see and hear him). Any caster in an unobstructed line within 30 feet does not require any Listen/Spot rolls. The DC is 10 plus 1 per 5 feet beyond the minimum plus 1 per opponent in a straight line between them and the caster. So, 2 opponents between the PC and the caster 50 feet away is DC 16. If the PC makes either roll (if he can both see and hear), he then can make his normal SpellCraft roll.
Course, enemy casters can do things like stick their head over a wall and then the PCs do not get a Spot roll (not being able to see the somatic components), just a Listen roll.
So in answer to the original poster's question, forcing your PCs (and NPCs) to make Listen/Spot rolls to hear/see the casting before making a SpellCraft roll can make illusions a little more useful in combat. It's hard to make your SpellCraft roll is you do not even get to roll it.