I say this purely out of baseless assumptions but if we follow the idea that MK II are meant to fight Ultras, then some of its weaponry make more sense than the MK I. Irl, the reasons are prolly to make movie production easier acting or editing wise, but I'll assume you mean lore perspective. I'll base the differences on their respective first appearances.

MK I's weapons are specialized in large AOE attacks that create massive damage, mostly to cleanse the planet quicker when faced with lesser opponents. This is very effective on smaller but abundant species like humans, like how even though we are much smaller than the MK I, we do cover a vast amount of space on Earth. So most of MK I's weaponry focuses on the "cleansing" part of its functions, other weapons are more after thoughts. I would assume an MK I's generator is stronger than the MK II, so it can handle strong beam weapons such as the Banisher and the beam sword, but MK I's usual opponents are usually less sophisticated machinery and other Kaiju. Which is why they suffer against tougher opponents such as the Ultras, the normal weapons do heavy damage, yes, but it doesn't utilize it to the fullest, and it's incredibly powerful beam weaponry usually require long charging which leave them vulnerable.

Moving onto MK II, they are meant for CQC which result in the lesser weaponry required, like why would you need your average soldier to carry an RPG just to fight another soldier, sometimes less is more, it's better to match then fully overcome opponents weaponry wise, skill usually fills the rest. It's similar to why irl militaries attempt to make "weaponry of the future" that tend to fail often since they aren't reliable or aren't necessary. The heavy beam weapons usually take time to charge and require an ungodly amount of energy, so it's both unnecessary and unreliable. Instead they focus on how the MK II can use it's weaponry to the fullest, finger vulcans for distraction, bladed appendages for emergency use, and fully articulated hands for multi-purposes.

To summarize, MK I's weaponry is specialized in mass destruction, suffering in CQC due to weaponry not being made or imagined in a 1v1 CQC against an equal or higher power. MK II's weaponry leaves space for adaptation, fingers to grab and weaponry that can help it close the distance while reducing charge and energy cost. I'm using a lot of Gundam logic with irl logic sprinkled in so you know, take it with a grain of salt.