I don't think standing behind another creature should provide cover against a fireball or lightning bolt either, but that is what the rules plainly state.
Table 8-9, PHB p. 133: "behind a creature of same size" = "one-half cover" with a +2 Cover Reflex save bonus.
"Cover Reflex Save Bonus", PHB p.133: "Add this bonus to Reflex saves against attacks that affect an area, such as a red dragon's breath or a fireball."
Lightning bolt spell description, PHB p.222: "Area: 5 ft. wide to medium range (100 ft. + 10 ft./level); or 10 ft. wide to 50 ft. + 5 ft./level".
Fireball is expressly given as an example, and lightning bolt affects an area.
I can't find anything under "Area" (PHB p.149), "Line of Effect" (PHB p.150) or anywhere else that provides an exception for fireball or lightning bolt.
So by the rules, creature 2 in your example gets a +2 to its Reflex save. Anything else is house rules - warranted, maybe, but definitely house rules.