I already did this about two years ago with my climbwar maps. You're not going to do it with trenches -- use colliders to provide cover from fire. Climbwar 4 is what I'd say would make the best example of how a normal,
balanced vertical CTF map should be made:
http://soldat.planets.gamespy.com/map/1392My climbwar maps played very similarly as the trenchwar maps did -- you're fighting for position and using objects to hide behind while advancing. This was the basis of !Elite Party, which failed since the server would always fail to load the custom maps for people.
http://soldat.planets.gamespy.com/map/3083Climbwar 3 was a split vertical CTF game in which each time utilized different means to achieve the CTF objective. Again, these were the first of these maps, and certainly the looks could be improved (as I did when I remade this map into inf_climbduck, an INF Duckhunt map for IQ Unlimited's server) as well as the layout (Bravo does need some more room for positioning).
Not posting to toot my own horn or anything. Those who got a chance to play these maps really enjoyed them once they got used to the premise, and I'd love to see more vertical CTF maps in this mode. It's a lot of fun, and it's great to have this kind of gameplay with most of the players confined within a screen or two. Unlike trenchwar, which relies more on blind spray and shots to advance, here you're visibly jostling with the other team to advance.