Three of the largest men I have ever met in my life happen to be sempai at my dojo; one is my sensei. I don't mean 'overweight;' I mean, 'built like semis.' One has hands so big that my thumb ends up closer to the knuckle of the second finger, rather than between the last two, when I'm trying to do a kote-gaeshi.
What I have learned in working with them is that I have much less room for error. Sure, a big, burly guy who clamps down and thinks 'I'm not gonna move!' (read: easily impressed beginner) isn't too hard to deal with, but add balance and awareness to said burly guy and I begin to have a problem. I don't think, though, that weapons are the answer; any blow I produce with a bo or boken is going to be less powerful than that of a stronger person of equal ability, just the same as a blow from my hands.
Does this bother me? A little. One of the first things I learned in aikido, however, is that Attacking Is Stupid, and very difficult to do without leaving oneself vulnerable - no matter what one's size.
Furthermore, I also know that aikido (at least the physical part) or any martial art isn't much good about someone standing 20 feet away with a gun pointed at you; is that scenario too much less likely than being attacked by a huge, highly skilled ninja (or aikidoka) in a dark alley somewhere? That's only somewhat rhetorical; if anyone has any data, I'd welcome it.