I was talking with Chris Da Wolf last night about just this issue. Spy and Engie are the two classes I have a hard time coming up with balanced unlocks for.
The Engie becomes a slow Scout without his sentries; the whole bonus of Engineer is that you can shoot something from two angles, or shoot something that you are not looking at, and that you can supply your team on the front lines. Most maps are designed in such a way that having no Engies to refresh your ammo and health (even with Medics), and do you really want to lose the teleporters? You remember how sad it was back when you couldn't level 'em up and nobody ever built them?
The Engie-Spy mechanic is already pretty darned tight. Sure, a sapper is easier to remove than it is to sneak up to and place, but you can sap four different pieces of equipment, and I have to triage. And knocking off the sapper doesn't repair the building, you can just come back and try again.
Every idea I hear for Spy or Engie always comes from one-side-players. "I want a remote control sapper where I can sap from my friendly battlements!" "I want a sentry that can see cloaked spies!" "I want sappers with permanent glue!" "I want a wrench that shoots bullets!"
It's hard to come up with balanced unlocks for those guys
I would like a hacker sapper that just disables buildings for double time, takes double the effort to strike off.
I would like the Engie to be able to place armor on buildings (think overheal), but I think sappers should only work on the base "health."
I'd like the Engie to get an automatic pistol or rifle. The pistol is cool, but my finger is about ready to pop off striking M1 at a million miles per hour. It fits; I can imagine the Engie building a superior gun. Or maybe TFC's railgun.
I like the idea of cloaks phasing through people, but it should still shimmer.
I like the idea of a silenced gun for the spy. No loud report, but it does 1/2 damage unless you shoot in the back. I'd even allow this to be shot while cloaked.
I can't imagine an alt for the butterfly knife... although I liked the idea of a garotte, that does 50 HP damage a second, and after you kill that guy, you get his costume and name. I think that would be too much harder with less benefit.
Anyway, adding cool unlocks have been easy so far. But Engie/Spy is quite well balanced, and already pretty useful to the team as-is.