Except it didn't presume that; it only presumed compatibility with 3.X while offering a facelift. It made some adjustments - adding more layers as time went on - but it was not created to "fix" anything. It existed to maintain the 3.X framework that Paizo could use for their own publishing purposes.
Combat is the most heavily emphasized pillar of the game. Our understanding of the rogue has changed partially because tabletop roleplaying does not exist in a vacuum. And in so many other media, namely video games, rogues have already made the transition to something akin to a combat striker.
Before 3e came out and people started complaining about an underpowered Rogue, which CRPGs did this?
James Bond would have been more of an Assassin or maybe a Ranger (an argument might even be able to be made about a Paladin and almost definitely more akin to a Monk or Mystic in earlier versions of D&D) class, which arguably was different than the Rogue class. Even up until 3.5 the assassin was still a prestige class that even a Fighter or Wizard with the right skill points could enter into.
Most characters people list as Rogues in defense of Rogues fighting either didn't fight all that much or were actually better classed as other classes.
For example, Batman is most definitely more of a Monk than a Rogue.
The original official Stats of Gray Mouser had him as a Dual-Class being a High Level Fighter and apparently originally a Fighter first, and then dualed into a Theif (F/T 11/15). He actually also was a 3rd level M-U/Illusionist. [his companion also a Fighter Thief, with their Thief levels being 13th level and their Fighter level being 15th along with being a 5th level Bard]. In AD&D, Gray Mouser actually got much of his combat ability from originally having the Fighter levels.
Many of those rogues that one saw in Early D&D that were good at fighting were either multi or dual class to also have high fighter levels.
This was because Fighters were the domain of combat. Up until 4e, Rogues were specialized in other areas, for example, 3e they were supposed to basically be more of a skill monkey type character. Most didn't care whether this was changed or not and played Rogues because they liked them.
A HEAVY ONLINE presence of people who hated this mechanic were very vocal about it, but that still is mystifying. A grand archtype of fantasy and medieval fiction has been the sewer rat, the rogue, the street urchin thief that scampers away from combat and isn't really a great fighter, but has many hidden qualities that turn out to be far more useful (street smarts, etc). If one wanted to play a combat guy they already have the fighter. Arguably I could see tuning up the Monk (so you have your ninja types, your skirmish stealth types...etc) for combat, but the Rogue fit an archetype that it seems many do not understand or even comprehend in our modern audiences for RPGs (though arguably the rest of those who don't play RPGs still understand it as it still shows up in TV shows, fiction, and other aspects of media).
A Rogue may not be the worst fighter (many CRPGs have rogue like characters which are decent, and are better at fighting than say...a Wizard or Magic-User [or white magic user for that matter] but are worse than at fighting than the martial types (though even a Monk type character is better than a Rogue in many games) but have other items. For example, in Final Fantasy type games they normally are good at swiping or stealing things from enemies in combat. They are not terrible at combat in those games, but are not the forward frontline fighters the martial types are.
This idea that Rogues = Combat class just as good as a warrior is kind of a weird obsession of TTRPGs and specifically D&D in the past few years. Rogues may not stink in combat, but normally the Warrior far exceeds almost any rogue in actual combat.
In some ways I think it roots directly where they tried to make a Rogue specifically geared as a combat type class in 4e. It had some abilities out of the norm, but it was more geared for combat comparative to a Ranger and others and labeled as a "Striker" akin to a martial type class rather than what a Rogue had traditionally been. Great for those of the 4e mindset, but I'm not sure why the rest of the RPG players bought into this idea, especially with how some of them eschew 4e.
