Good Lord, if that was real life it would be called discrimination, it would take away many of the spies main tactical advantages (cloak, disguise, sapper become null, or at least hopelessly inefficient)
On topic: I think the engineer would do well with a:
'Texas Longrange' sentry.
This sentry has 30% more range as the normal sentry at level 1, at the cost of reduced rate of fire.
At level two it would be the same, but at 50% more range, and slightly higher rate of fire
At level 3, rockets are removed or nerfed, and the range is double that of a normal turret or 75% more range, and turrets rate of fire is increased slightly (Still lower than normal sentry) and at level 3 it gets its lovely double miniguns
EDIT: Someone done this, ah well, personal take on it
The team-iporter:
This replaces the teleporters, it does the same job as a teleporter, but can teleport 2 people into battle, at the cost of a higher recharge rate,
At level 2 it will teleport 3 people
This will be extremely helpful for heavy/medic combos who want to get straight into battle without the bother of walking at heavy speeds.
Replacement for the wrench could be a:
Rivet gun. Runs on metal, heals buildings at range each rivet repairs for 10 metal, with the repair amount experiencing dropoff the further away you are from the building, and yes, it can be used to kill people.
The Brander
This lovely weapon would take the place of the pistol, similar to the demoman and his sword, it has a high damage output, at the expense of lower rate of fire, if you will, in return of a lower crit chance/no crit chance, it has the alt-fire of branding, which will cause a smoke trail to come from the enemy hit by it for a small time, very useful to see where scouts/spies have run off to.
Will edit if i think of anything else.