It's an interesting thought that changing a single item slot would make gunners obsolete. Already there's a lot of debate on whether they're obsolete already. The idea of the gungineer isn't necessarily to replace the gunner (although that's not such a terrible thought), but to fill the role players are already being put into; the gungineer. So you'd have your engi, gunner, and gungineer. Except you're probably right when you say players are likely to bring two gungineers and an engi. All I can do is shrug at that.
As for watering down builds by increasing variety... eh? Right now we already have 'standard' builds. A large portion of pilots bring kerosene, phoenix claw, and one other; along with a spanner/pipewrench, and some ammo type they'll almost never use. Standard engineers have a spanner, mallet, fire ext, spy glass, and an ammo. Gunners actually show the most variety, but even then it's pretty standardized based upon the weapons they're going to be using, having a pipe wrench and spy glass along with it.
You can't get much more standard than that. Allowing more variety increases the number of possibly combinations. You'd certainly have 'standard' sets pop up, just because players like something familiar, but I think you'd see that less than you do already.
As a captain, you could opt for 3 maneuver tools, a spy glass, and a repair tool. Or 5 maneuvering tools. Or 4 and a wrench. Or 3 and two wrenches (such as if you were going to be in charge of repairing the balloon).
Players doing a repair oriented role would often go spanner, mallet, fire ext, buff, ammo; but they might opt for spanner/mallet, fire ext, chem spray, ammo. Or spanner/mallet, fire ext, buff, spy glass. Or range finder. Or bring all the wrenches to optimize repair times.
Then your offensive players would go for some ammo types (probably two), followed by more repair and maybe a spy glass. Maybe only 1 ammo type and more repair. Maybe they'll bring a spy glass and a range finder along with their ammo and a wrench. Maybe two ammo, a wrench, a buff, and a spyglass.
Suddenly whole new combinations open up. And as the amount of items increases, the possibilities expand as well.