Engineer's alternate buildings replace the entire set of buildings, rather than any single one. Here is what I came up with for a more teamwork-oriented and situational Engineer loadout.
Sentry replacement: Force Field Generator. Generates a spherical region through which (undisguised, uncloaked, possibly Bonk!ed) enemies and their bullets cannot pass. The range of the sphere increases as it levels up, but never matches the range of an ordinary Sentry. Any attack on the force field reduces the radius, and if it reaches the minimum the generator is destroyed, but it regenerates over time. The reduction in the radius is not directly proportional to the amount of damage done, but is balanced to make less effectual classes capable of taking one out. An Engineer repairing the force field trades metal in exchange for more quickly replenishing the radius. Enemies within the force field are not pushed back and can damage the generator, which will break it faster, and which will not automatically be undone, but will not diminish the radius of the field at all. It does not function while sapped. Enemy sentries may or may not automatically target force fields.
Teleporter replacement: Jump Pad. Pretty straightforward. You get a preview of the arc it'll send allies on. Only the Engineer that planted it can take falling damage from it. At level 2, it recharges instantly. At level 3, allies are immune to weapons fire while in flight, as with Bonk!, and if they hit an enemy in flight, that enemy is telefragged. Possibly, the angle can be adjusted prior to or after construction.
Dispenser replacement: Remote Control Terminal. One allied Engineer - but (possibly) not the Terminal's builder - can enter the Terminal at a time. That Engineer selects one of his own buildings, and can move the building around in real time. The Engineer is highly vulnerable during this time. The selected building continues to operate as normal while moving. If the building is destroyed while being remote-controlled, the Terminal is subject to recharge time, which can be hastened by whacking it (possibly costs metal). The higher the level of the Terminal, the faster the building moves. The speed might also be influenced by the type of building being controlled. At its fastest, it should go no faster than a spun-up Heavy. At level 2, the building gains the ability to make a small jump; at level 3, it gains rocket boosters that can take it as higher (maybe ridiculously high for the smaller buildings, if their speed matters at all). If a mobile force field generator squashes an enemy in a corner, that enemy will die. Mobile buildings cannot enter no-build zones, and they cannot travel through teleporters or jump pads, nor enter enemy force fields.