Scout is my most played class, so I'll just keep it short and simple:
Scout may have the best capture speed, but by and large the Scout is designed to kill. That's his best job. In a 1-on-1 with any other class in the game, at the highest skill levels, the Scout will always win.
As a result, what helps the Scout most is a supplement to his firepower, and the Pistol does this the best. It add damage that will finish off an opponent when reloading is not an option (i.e. you're out of Scattergun or you were using the FAN and didn't finish the job right).
The Crit-A-Cola is somewhat useful, but its ability to have yourself hurt more makes you rely on using it in ambushes rather than direct combat. Just by having to rely on ambush, you already greatly limit the Scout's combat potential. It's just not very cost effective.
And Bonk! is only useful if you're playing constantly playing the Sentry-distractor Scout, which is an extremely niche role and can be filled by many other classes by themselves.
Alright, so your argument is a good one, certainly, but there a few things I'd like to discuss here. Note that because the discussion is so one-sided here, I'm going to try to flip it around a little bit.
First thing is just a matter of absolutism that I'd like to get off my chest: in a 1 on 1 battle between scout and any other class, at the highest levels, scout will certainly not win every time, although he'll probably win more than half. The cases I can make here are for the heavy; any competent heavy with any kind of mouse sensitivity will negate the scout's speed. Even if they don't hit them with every bullet, the scout doesn't have a lot of health. Even if you get the jump on him, the odds are against you there. Scouts also may have trouble against solid soldiers, because they don't need to hit them dead on for their damage to work. I could probably make cases for most classes, but not all; demos, for instance, will lose 9 times out of 10 to a scout.
In any case, I think it's a little naive to suggest that one class will always beat all of the others in a one-on-one scenario; if that were the case, the game wouldn't be balanced, and everyone would be playing scout at the competitive level.
Now, as far as the actual subject of this discussion:
As far as the combat role of the scout, I think opscomm said it right. The scout, as far as I'm concerned, is a hit and run class. Scouts shouldn't be leading the charges, they should be flanking. I think because I believe pretty staunchly that a scout CANNOT take each class 1-on-1 with a good chance of winning, even assuming equal skill, the scout's best chance at doing well is flanking. For instance, in mesa, when your team has 4 points and are just coming around the corner to the hall with the windows, scouts probably shouldn't be coming through that narrow entrance with the whole rest of the team; they should be running through the vents to get to the room above spawn, or the at least the window room connected to the vents. This is so that they can get people from behind, pick on them when they're weak, and generally cause pain from where the enemy isn't expecting it.
This idea is reinforced by their mobility; just like the soldier, who is actually faster than the scout when played well, they are built to out-maneuver the enemy.
So, with this idea in our head, why NOT crit-a-cola? If you're dropping down from that area above spawn in mesa to get some people in the back, having 6 seconds of mini-crit, I would contend, will be more useful than having a pistol. Yes, you're more vulnerable; really more of a glass cannon then you already are. However, 6 seconds isn't all that long, and in practicing a hit-and-run style of play, you'd likely do well to pop off a few shots, and run away.
Bonk is a little harder to advocate for. I used it for a long time, and it's situational uses came up more than you'd expect. I have killed engineers with their own sentries, certainly, but what's MORE interesting is that I've blocked ubers. finding narrow passages is great for this, but even open spaces work, assuming you get up in their faces and block as many bullets as you can (in the case of pyros and heavies specifically). 6 seconds is a significant portion of 10, and generally speaking, if you do your job, you've wasted an uber pretty effectively.
To all of the pistol users, I have a question:
You argue that the lunchboxes are very situational, and I don't disagree with you. I think that they are. However, how often do you actually find yourself using your pistol? once a life? once every 2 lives?
Maybe your playstyle has adapted to incorporate it more, but generally, I like the idea of stealth. If I'm going to go harass some snipers, especially if I'm coming from another direction, I don't take out the pistol; I get right up close and personal, and shoot them in the back with the scattergun. same goes for most things. Plus, I find it rare (especially using hit-and-run tactics) that I run out of ammo on the main gun. I'm constantly reloading, and I don't fire until I know I'm going to make contact. because I like to flank, it means I only tend to deal with one or two people at once; 6 bullets is more than enough to deal with that before running away to reload.
So, for these reasons, I rarely find myself using a pistol. It's useful for taking out long-range sentries, but the chances of that occurring are fairly situational; as situational, perhaps, as having to use bonk on a sentry, or having the opportunity to safely use crit-a-cola.
Edit:
*facepalm*
I'm pretty sure EVERYBODY has that same opinion.
Touche.