In manga, stories, movies, + television, it's actually quite common for scientists not necessarily smart enough to come up with technology way beyond even their understanding, and ends up shocking them with what their capable of. Hell, to this day, Dr gero never seemed smart enough to create Cell in the 1st place.
As for his metal, + if it's the same, you don't know either way, do you? Cars before were made of very dense heavy metal, yet cars nowadays are made of lighter metals and it's considered "progress", even though that light type of metals and "even better mass produced" more eco-friendly materials actually provides that car accidents are even more deadly to those within and without the car. my point being, sometimes the proto-type can better, than the end results in unforeseen ways, + with Kuma being as different as he was in the st place, he is still obviously superior to the rest anyway. Not to mention if Dr. Vegapunk really is evenly decently intelligent, he would still put more effort into making Kuma stand above the PX's, not to mention the upgraded 1's Sentoumaru mentioned.
You said, during those 2 years he never got upgraded, but isn't it feasible that PX's, or even beings, or groups, as strong or stronger than PX's were sent to get that ship? Yet he stopped them all possibly for times non-stop time for some sort of break between attacks. You really don't think he deserves credit for that, in being above pretty much any PX? And now he can have updates. You don't think he got them? In fact, these upgraded PX's, have you ever thought the way they updated them was with more creative thinking, + reasoning, possibly something resembling anger, ( for added power), + strategy? Meaning when Kuma gets such updates, he could be as or even more dangerous than he was before, as well. CM, you seem to act like if Kuma didn't or doesn't get updated right away, he could never be possible of competing with other Shichibukai, when simply that isn't true.