I once ran a tournament module at a convention where something like this came up.
The local conventions used to have tournaments where the same module would be run on a dozen tables at once, three times a day, so the author was rarely the one running it.
In one scene there was a corridor with barred cells lining it. In one of these cells were some Slaad. There was a trap at each end of the corridor that opened the cells. It was expected that the party would spot the trap as they entered and neglect to look for one as they left. I realized that the Sladd in question all had the ability to throw Delayed Blast Fireball, which they could shoot right through the bars. They were also personally immune to the spell.
If they fired them at once, it was a TPK. Very bad adventure design that I decided not to abuse.
Instead, I waited for them to spring the second trap (they did). Then two of the Sladi leaped out into the corridor. One of them screamed, "Die Wizard!", as he hurled a small projectile at the party magic user (yes, it was 1st edition). The marble-sized sphere struck the spell caster in the chest and dropped to the ground harmlessly.
I described all of this, and tossed a D20 onto the table, indicating that the sphere was about that size.
The larger Slad slapped the smaller one, saying, "You blew it Stanley!". The smaller one whimpered, "I'm sorry Ollie, but you said to...", and they began to bicker.
The player of the Mage who had been "attacked" picked up the D20 and declared that he was examining the sphere.
I asked what others were doing, as I visibly counted down with my fingers on the table top, not waving the count down in the air to draw attention to it, but not hiding it either.
When I reached zero, I asked for a pause, and explained that the rules gave the DM some discretion regarding Saves and situational modifiers. For example, throwing a Fireball at someone waist deep in water might give them a bonus on the save, while a Lightning Bolt thrown at the same target might call for a penalty. So I asked, "What do you think the Save penalty should be for someone holding a Delayed Blast Fireball six inches from his nose when it goes off?"
Much laughter, and an acknowledgment that the Wiz in question was pretty much toast.
In that case, they had plenty of time to see what it was, make guesses and/or appropriate checks, take cover, whatever.
A non-delayed spell, however, gives zero time for consideration, calculation, coordination, or anything else that begins with "C" (like "Cover"). Everyone is "flat footed" every time. Unless you happen to spot the casting and make a good Spellcraft check, the effect is always a surprise.
Trying to decide that some people are more flat-footed than others, and penalizing them for it, seems like a DM wanting to punish players for, well, for something.
There are already modifiers in the rules for a lot of this. Unconscious? Zero Dex and no Evasion. Slowed? Reflex Save penalties.
My own group took a different tack, by the way. We disallowed Ring of Evasion. That item, at higher levels, makes area spells pretty much useless. By limiting Evasion to the classes that have it as a class feature we eliminated the type of angst that frequently seems to lead to discussions like this one.
(Tangent: If you want to see how Evasion works, see the Indiana Jones film, "The Crystal Skull", and how he survives a nuclear blast. Then throw up in disgust like everyone else did!)