Myself, I fall into Patryn's second camp. Grapple checks are like melee attack rolls but with a different size modifier. Anything that applies to a melee attack roll applies to a grapple check. (When Skip was writing, the FAQ seemed to agree with me, now that Andy is writing it disagrees, oh well).
The basic question comes down to which of the following situations you'd rather see come up in play:
1. I've taken eight negative levels, I'm shaken, and I've been hit by both bane and prayer, and I'm prone. Ordinarily this would mean that I'm -16 to attack, but I know, I'll start a grapple. If I can make the touch attack (and touch attacks are easy), I won't have any penalty to my grapple check because grapple checks aren't attack rolls (or strength checks) and thus none of the penalties apply to grapple checks.
2. Ouch! That blow hurt a lot--he must be Power Attacking for a ton. Well, at least it will reduce his grapple check; I'll start a grapple and seeing as he must be at -12 or so, I'll have a good shot at getting him (at least until he stops power attacking).
Myself, I prefer to have the penalties from Power Attack (and Combat Expertise though that's a little less intuitive) as well as fear, bane, prayer, negative levels, etc (really, the last two SHOULD apply to grapple checks, but according to the "neither quite strength checks nor attack rolls so no penalties from either" logic of the FAQ, even penalties that apply to everything else in the game (skill checks, ability checks, attack rolls, etc) don't apply to grapples) as well as the bonuses from such effects change grapple scores. Some people apparently like it differently.
From a rules standpoint, it's also worth noting that both attack rolls and grapple checks are described the same way in the PHB: d20 + BAB + size modifier so the fact that the grapple check description doesn't include all the odd bonuses that can affect it means no more than that the attack roll description doesn't reference them.