Sadly it doesn't sound like you guys ever have experienced the classic TF CTF gameplay in organized teams, so I think you are underestimating the many elements that made that game unique and exciting (and completely different) than say dustbowl A/D.
TF2 punishes death highly, and due to the mechanics of the medic and uber it drastically changes how CTF plays at the top level. Instead of layered defense and a fast paced offensive attack it becomes a very conservative push and hold game with one ginormous blob. If it's a push and hold game it might as well be CP, because that's what the mode is suited for and that's how it plays.
What the mode I'm proposing would do is open up the door for more aggressive play on offense (because they don't have to worry about the other team steamrolling to their flag if they fail) as well as bring back some of the CTF excitement of flag pulls...most importantly it helps improve the pub game experience.
There are other elements that could be improved because a lot of the CTF maps in TF2 are in cramped low ceiling flag rooms leaving little room for finesse flag grab attempts, but those could come with time.
I played competitive TFC for about a year and a half. Not at the highest level by any means, but it was at least above the "just playing/joking around" tier, I played defense, soldier.
TFC is a completely different beast from TF2, it's not comparable, and with these new fundamental changes to gameplay, the traditional ctf model just doesn't work anymore.
To understand why you can't emulate TFC ctf in tf2, I need to explain TFC (for those who didn't play it):
Flag capping in TFC was basically 4-5 medics*/scouts throwing themselves at a defence (4-3 players) over and over for 30 minutes and then at the end seeing which team got through (and out again) the most.
That kind of gameplay is impossible to sell today, no matter how you disguise it, it's very repetitive and the reward is low, while extremely high paced and difficult.
*medics in tfc were more or less a slightly tankier version of a scout
Either way, there's something important to note here, the battle was extremely one-sided (but happened on both sides of the map, think of it as two 4v4 matches happening at the same time). The attackers had extreme tunnel vision on the flag at all times, the best strategy was to zoom past everyone and everything, flying through the air, if possible. IF they got the flag, the goal was to move it as far as possible, each attacker would come in after each other like a relay race, moving it further and further until it was out of reach for the defense (unless the flag got stuck in some corner, it was pretty rare to see a flag return on its own).
There was never a real conflict between A and D. If a attacker messes up their route they suicide themselves, if a defender lets a guy past, and he's out of health/armor/grenades he suicides too (any of the 3 is a valid excuse to do it), as long as he's back on his post before the attackers come back.
Ok. I'm done. What were we talking about? I got lost in thought, remembering tfc... I think I had a point to make when I started writing.
whatever, have a cool video with ancient music
http://www.youtube.com/watch?v=4rDht5JmKP8 (that that this is a highlight video, not shown is the millions of deaths where he just get exploded by all the rockets, grenades and sentries)
Oh right, I remember:
What you'll end up with (if I interpreted your post right), is something that plays like very much like stage 3-2 of dustbowl, or any other final cp of a A/D map where the defense has a big initial advantage. You'll play that single point for 15 minutes then switch sides, and count how many times blue managed to get over there and capture the point (let's say it resets to red ownership after each capture).
It has exactly what you're looking for, shorter respawn times for attackers, and opportunity for teleporters even. And a clear goal for both teams.
Just because you make it a flag instead of a cp doesn't make much differance. It will not change much in terms of how teams approach the problem I think. A minor tweak in the gamemode doesn't suddenly change the whole metagame of ubers and airblasting and krtiz stickies, wrangled sentries, healing and just general pushing strategy.
edit: I missed this post:
Assuming the defending team is going to cluster deep inside their base and fail to meet the offensive team at the periphery of their base is unnatural. A layered defense with forward holds at choke points is typical to CTF. A layered defense means that supposing the outside layer is passed by some offensive players, they then are dealing with flag room defenders. The outer defenders will respawn before it is possible for the offensive players to clear out the flagroom defenses and exit with the flag. If the defense is choosing to pack everyone in the actual flag room then they are playing suboptimally and they deserve to lose the flag in one fell swoop. That is a rare occurance to get a "coast to coast" and I'm not sure why you think it would suddenly be the norm. It would be even less common once you take all those people that mindlessly dm in the midfield and have geared to protecting their flag.
The more I think about it, the less useful a outer layer of defense sounds.
Assuming it's 6v6, typical comp-tf2, maybe with some heavies and engineers where fitting, it's pretty easy to see how a team that DOESN'T split up will have a much easier time killing dudes and then dominating the flagroom and capping.
Putting 1-2 people in a outer defense just makes them easy kills.
TF2 has medics and ubers. And generally in tf2 you push and gain ground, you don't rush and solo the entire enemy team.
TFC had layered defence, but as I explained earlier, the attackers didn't actually fight the defence, you ran past it, if you could. It was more of a gauntlet and not a push into the flagroom.
