I know this has been suggested before, but not being able to use spies on Minor races puts the player at a huge tactical dis-advantage compared to being pitted against major races, espically when you have a mega-event such as the Jagged Knife.
In a recent TA game, they took 30 of my planets. Not a big deal, but I use spys as scouts, to see which improvements and terrain types have been laid down. This is espically important when, out of hundreds of planets, I've forgotten which ones I've put GA and Wonders on. Being able to see the planet helps me decide if I want to spend my resources retaking it, and what sort of invasion tactics to use. In other words... This is a strategy game, and by removing this feature, for me, you've removed a level of strategy. It then becomes a brute-force issue of 'hit everything you see with as much as you have.'
Additionally, it's out of sync with the 'in character' elements of the game. While it may not make sense to waste spies on sabatoge for minor races, in these rare circumstance, such as a Jagged Knife incursion, it's just plain stupid not to. When some race, minor or not, takes over 1/4th of your empire, you're going to bear all your weight down on it. When the Drath only have one planet, which I can spy on all I want, and I can't spy on a 60 planet strong nation, something's wierd. Also, as supreme-uber-poobah of my civilization, I'd like to think that I could stick a spy on a minor's planet over the objection of my trusted, though tactically inept C3 protocol droid.
Hell, while we're at it... It'd be nice to have the option of disintigrating my robot advisor, just like a Hutt. Just an option on any screen where he appears, with a nice satisfying animation of him being blasted to bits, or jettisoned into a furnace, or crushed. Perhaps you could have the option to use him as a one-shot ammunition from your flagship, or have him refurbished as a genisis torpedo to terraform a planet. In short, I want to be able to force-choke my councilors. (Guesses at my alignment, anyone? Suffice to say, I can't party with paladins.)
Anyway...
I like the Mega-events. I even don't mind the Jagged Knife. I love the challenge presented. I'm not opposed to arbitrarily changing the rules of engagement in the middle of the game, so long as they don't fly in face of common ense.