What you've said about 2fort may be true, but that's the exact consensus I got when asking people why they hate 2fort so much. The big problem with 2fort's design can be split into two branches, which route you'd take the intel topside.
Through the spiral stairway, It's a long climb around a narrow corridor. I've yet to see any remotley competent defense fail to stop an intel-stealer going up spiral. And then what? You've got the intel sitting in the top floor right outside the enemy spawnroom at best, or inside the said narrow stairway at worst. Either a miracle crit spree for the offense team happens, or the defense has to suddenly become amazingly stupid for the intel to budge an inch in there.
Through the courtyard is the more viable option. Unfortunately, those sentry guns you destroyed to get up through the courtyard and into the basement? Yep, they're back, and you're likely to drop the intel on the doorstep of the upper level instead of the courtyard floor. No team is likley to swarm soley around the courtyard if their intel is dragged there. You've still got the defense on the battlements for the express purpose of denying soldiers/demomen entry. All that really happens is the defending team (for the most part) stops attacking the other team's base. Sentries are still a nightmare, especially if there are two guarding the courtyard.
That a team's flag should be put in extreme jeopardy ought to be punishment enough for their defense failing them. Their "second chance" should be granted to them only when their flag is returned.
Now, Checkpoint on the other hand....
The intel room is designed so that no single sentry can effectively defend the base by itself, by splitting it up into three sections. One sentry inside the middle (valley) has no hope of defending the outer walkways. One sentry placed on either walkway has no hope of defending the middle, or the other walkway. Even two sentries placed in either section have no answer to an attack coming from the undefended section. As opposed to 2fort, where two sentries in the courtyard would pretty much lock the whole place down.
Now, addressing the spawnroom question. The spawnroom was designed so that any class could just get out and go at it quickly, but hindering Engineers running back to the cabinet for a quick metal restock (And the hole is big so that people would notice it :/ ). Like Valve's commentary suggested, you either take the long, safe route, or the short and dangerous route. Taking the "Navajo long walk" up to the resupply cabinet is the long and safe route for Engineers. Venturing outside the base for metal is considerably more dangerous but quicker. This forces Engineers to build their stuff in a horribly inefficient manner, and leaving their buildings unattended for extended periods of time. Obviously the ideal place for a Sentry would be inside the valley. But this extends the build time and the time spent away from the sentry. The quicker place for Sentry building is in the walkways, but it leaves the valley (and the intel) completely undefended.
Plus, once the attacking team has the intel stolen and on it's way, they don't stick around very long inside the base (unless the defending team is bewilderingly incompetent)
ETA: Also keep in mind that this map was originally designed with the Competitive CTF Contest in mind, with fast caps as a priority