Mangy, this may have already been mentioned to you before, but I would suggest adding the circular dynamic arrows used on tc_hydro ("models/props_hydro/cap_point_arrow.mdl)". When BLU has the intel, activate the blue arrows and have them point toward RED's base. And when RED has the intel, turn off the blue arrows and turn on the red arrows pointing toward BLU's base.
Also, whenever a player picks up the intel, I'd suggest using game_text_tf to display a message that effectively says "Take to ENEMY base". A game_text_tf message gets displayed anyway whenever the intel is captured, so this would be somewhat consistent with existing ctf mechanics. If players find it annoying, they can always turn on the Minimal HUD, where it won't show up.
I like how you've set it up so that the intel automatically drops if a player takes it the wrong way. You might already plan to do this, but I would put some kind of distinct visual feature (such as a door that opens and closes) to better indicate where these intel-dropping barriers are. Also, it's currently possible (in a6, anyway) to go through a short drop-pickup-drop-pickup routine that will let you get the intel past this barrier, and then you can take it all the way into your own base. You might have to do some more design tweaking to prevent this.
Also on a non-layout note, you might want to consider getting a different model somehow for the flag. It might be able to help players establish that the map is different from standard CTF if they are not trying to give their teams intel case to the enemy. Maybe make it a bomb of some sorts. (Or being goofy, coal to throw in the other teams heater in hopes of over heating it to explode

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I agree with this too. I know that by default the game uses the term "intelligence" for various messages and displays briefcases on the HUD, which is a bummer for custom mappers. Maybe you could think up some kind of intelligence-related item that players would instinctively know to take to the enemy, rather than to take back home. I don't have any concrete ideas for you, though. Perhaps a "briefcase bomb" or maybe "sham" intelligence.
I look forward to the beta!
