One thing in the way is that CTF is a hard thing to integrate in the lore, but I can guess that it will have to do with data acquisition. Another issue is making the mode - traditionally revolving around single "runners", a tactical squad-based endeavor.
My answer? instead of a mobile flag, we have to download and transport data. I'll explain below

Espionage

Objective:
Download strategic datafiles from the enemy communications center(s), then bring it back to base. Victory is attained when enough data is stolen.
NOTE: Primary objectives in this mode cannot be flipped to the opposing team.

Downloading:
When you reach the enemy objective, initiate "hacking" mode to begin downloading. A display on your screen shows how many Terabytes have been downloaded. Once you are satisfied - or you come under fire - you can end hacking and try to return with the amount of data you managed to steal. As this is a "hacking" mode, Codebreakers increase your download speed.
As for maximum data storage per suit, it is up to CCP, as is whether there are methods to increase it.
Obviously, the data has to be re-hacked should you bleed out.

Data:
Although the MCC would still be present, this is the first non-Ambush mode where it is not the objective, and therefore allows player usage and fitting.
Instead of the MCC health on the HUD, you have a number representing the total Terabytes of data brought back to base
The enemies' captured TB counts could also require "querying" by hacking the upload base - which temporarily disables data capturing by the enemy as well. This means that a team can lose without knowing it until the Defeat screen. (query mechanic is strictly optional, added only for logic purposes)

Uploading:
Once you have returned with some data, the main command unit swaps our your suit's auxillary drive, after which you can immediately start going back to the enemy base. All TB stored on the suit is "captured" in one of these turn-ins.

Vulnerability:
Tactical data is well-protected, even by itself. Malware hidden in the code causes the carrier suit's sensor suite to fall out of sync, increasing scan profile. At maximum data capacity, a data-carrier is a big, glowing spot on the enemy's TACNET, and very easy to track. The same malware interferes with vehicle interfacing, preventing the carrier from using 1-seater vehicles after collecting TB past a given threshold. Multi-seat vehicles have redundant coding to prevent such issues.
This is the part where you need a squad to fend off the opposition while you high-tail it home in anything with at least 2 seats.
(vehicle restriction prevents players from using the fastest vehicles to capture with impunity)

Getting bigger:
On larger, MAG-scale or bigger maps, one could utilize multiple download points at multiple bases, with some TB being unavailable at a given one - requiring at least some data from other zones of the map to win. Not all are needed, as there would be some regional data overlap - as expected with a tactical data exchange system.

Summary:
>Hack objectives to gain TB, then return to base.
>TB is downloaded over time while hacking the objective. Hack longer to attempt to capture more TB.
>More TB carried wins faster, but makes you easier to track by enemies.
>Carrying more than a small amount of TB prevents you from using 1-seat vehicles like Fighters.
>Hack enemy "upload" point to query their TB count (optional)
>Can work on larger maps due to variable TB counts and multiple download points.

EDIT: this mode would act like a modified CTF on our current maps, but becomes a deep, strategic mode on larger maps where region overlap and vehicle dynamics come into play.
You only have to gain TB from a certain percentage of the bases on larger maps, allowing commanders to pick and choose which places to attack - or even perform misdirection to confuse and split defenders.

P.S. I can also modify it into an attacker-defender mode if need be - as it would support the future addition of gigantic, strategic maps better.