Who was it who mentioned that ammo types don't work together in the same way that engineering tools do? I can't seem to find the post, but I think they hit the nail on the head. Let's look at a light mortar, for example, which is a pretty popular gun to stick gunners on.
A gunner will take something like lesmok (for the range), greased (for the DPS), and heatsink (for fire prevention). This gives them some strong versatility, but...
An engineer can take lesmok, but then also have a buff hammer and chem spray. On paper this gives them the same abilities as the gunner (range, power and fire prevention), but the key difference is that all three of these can be acting at once. If I want to protect my gun from fire as a gunner, I can't do so at longer ranges because of heatsink's projectile speed reduction. Similar story with greased. The biggest draw of the gungineer is that they can stack all of their abilities together.
Of course, there are guns that work rather differently. The lumberjack, for example, pretty much requires a gunner (the one situation where I might disagree with that is on the lumberspire, due to how isolated the front gun is from engineers, and if the enemy gets close to your Spire, something's gone terribly wrong anyways). Still, I don't see arming time being a solution for most guns...
I guess we'll have to wait and see what Muse comes up with.
@Zenark: Actually most of the people who don't use gunners now have been asking for them to get buffed for a long time. What do you think the whole purpose of that massive thread was?