I just thought it would be interesting to consider. I write fanfictions, and i have a problem.

I just can't kill off major characters.....at all.

Any deaths that are major are always restricted to bad futures or off screen. What I need is a villain to take down one of those three.

Someone powerful, ruthless, and preferably an interesting matchup and unorthadox. I don't want to use Doomsday on Superboy, which is the backup plan

How about Prometheus?

from the comics dick grayson dies i think from someone altering time (most likley the black beetle) super boy dies from prime in the crissis i think flash lives the longest unless your talking about bart lol he dies too

I think a parallel of the JL/JLA storyline would be interesting. Flash was supposed to have been lost to the "speed force" or something of that nature and he was dead in many alternate universes (idk much about specific dc stories). So maybe doing the same to kid flash could incite a similar dramatic effect upon your readers.

kill all of teen titans, leave tim and batman

What about Holocaust. He took on an entire team of Titans and they barely could defeat him.

Deathstroke??