First, the PHB says that if it's used to raise the dead, there is no penalty. Why not? Usually when a wish is used to raise the dead, it's used more like a [/i]resurrection[/i] spell. So why not have the wish spell cause disability?
And the way the spell is worded, it's hard to tell if it means the caster ages 5 years when casting it regardless of what it's used for, but only causes the Strength loss if used for something other than healing, or if the weakness and aging only happen if the caster attempts to alter reality on a larger scale.
The -3 STR penalty is silly. Wizards don't need STR. Maybe a -3 to INT (mental strain) or CON (physical strain) from casting such powerful magic would be more realistic. A wizard with a 9 STR going down to a 6 STR isn't inconvenienced in the least. A wizard going down from an 18 INT to a 15 INT is mightily inconvenienced. Wishes should be draining.
So how do you all use it?
Personally, I vary it by campaign, depending upon player maturity, deadliness of the campaign, etc. But in most cases I insist on the 5 years of aging no matter what a wish is used for. The weakness is usually to the CON score, 3 pts, plus the 2d4 days of rest (which restores the CON score-nothing else will except multiple restoration spells).
