"They guard all the doors, they hold all the keys - which means sooner or later, someone will have to face them."
People always talk about how "at the end of M1, Neo becomes God, and then the sequel nerfs that again" - but what's rarely brought up is the way the M1 ending itself kinda goes against what the above exchange had set up.
Where did that whole "go out there and show people impossible things" come from, all of a sudden? The previous One didn't do that, did he - and earlier, Morpheus was talking about Neo having to fight through the Agents to get access somewhere, to presumably put a dent in the system or something.
All Reloaded really did, was retcon that odd and sudden ending that didn't match the preceding movie anyway, and instead pick up that earlier "keys and doors" concept again - albeit in an altered form, because now it's something the rebels apparently hadn't been aware of and is revealed to them by the Oracle and all the newly introduced rogue programs.
A good way to bridge the two, would have been Neo failing to get anything useful out of the agents the way Morpheus had thought (maybe the system reacted and stripped them of their access codes or something - or it turned out to be false info in the first place etc.); and then, as they learn the robot army is coming to kill them, Seraph, the Keymaker etc. start appearing and reveal all those additional hidden areas, the Merovingian's underworld network etc.
So yea, Reloaded isn't "the wrong sequel" anywhere to the extent it's often claimed - in fact, ignoring the original's problematic ending scene is the "wrongest" thing it does, in a way.