I think both sides have good arguments but according to the rules, you can decide exactly where your fireball will detonate (thus catching ennemies but not PC in melee with them). Just take a look at the fireball diagram p. 204. Mialee casts her fireball so that the spread will stop exactly in front of her.
However, I would agree to limit spellcaster's ability to judge distance so precisely. Fireball is like a grenade. You can spend your life studying the spread pattern of a grenade but no one in his right mind would throw one near his comrades (meleing with ennemies), hoping to catch the opponents only.
I don't think fighter types have as much opportunity to metagame when comes the time to judge distances. So applying a rule limiting the accuracy of distance judgement will not affect fighters as much as spell casters... Anyays, it is more often than not much easier to judge if you are at charging distance than to evaluate a 20-feet spread 400 feet away
In our group, we just ask the spell casters to be honest when they cast a spread spell. In crowded situation, we ask him to point an hex on the table without looking too closely. It gives a bit of randomness (you are usually able to have your fireball detonate where you want it, take or give 5 feet). Even the players would cringe if the wizard was about to cast a fireball so precisely it roasts ennemies that are meleeing with us without harming us.. And my barbarian would have a little discussion with the mage if he started to see fireball exploding just under his nose

Likewise, my barbarian counting squares between him and his ennemies to choose the best tactic would not be looked kindly upon.
Moreover, I think the area of effect of a fireball/lightning bolt is intended as a limitation of some sort. You won't always be able to cast it because you won't aways have the room to do so. That is why there are spells like Flame arrow. Same level as fireball, about the same damage (8d6 of fire damage at 8th level) but targeting only one creature per bolt.
Just my 2 cp...