Sounds like the additional armor and knife range in Blacklist is causing most of your complaints. That's also one reason I usually stick to Classic.
Regarding the knifing, I think the Mercs' guns need either better stopping power (so Spies slow down when they're being shot), or make it so Spies can't knife while being shot.
A slow down effect while being shot would definitely help, but Spies should not be able to knife-kill from the front at all. This wasn't allowed in previous games and it used to require skill to get behind a merc and pull of a melee kill. It was satisfying for the spy, and didn't feel cheap to the victim merc (you let him get behind you after all).
In Blacklist, there have been so many times that a spy is running straight fucking at me and I'm holding the trigger unloading into a them (and getting at least 5 hit markers) and the bastard still knifes me from the front.
I know, I should just "suck less"