Because Jones was extremely wary of the power of the MIB's energy weapons, he had expended a lot of effort to mutate his exoskeleton to make him almost immune to those weapons. However, it came at a great cost.
To explain it in simple terms, let's assume the Jones that had evolved to his peak form had 100 points of life energy. If he'd followed his previous direction of evolution, he'd only need to spend 10 points of life energy on his carapace. The remaining 90 points of life energy could be used to strengthen other aspects of himself.
However, to evolve a carapace that was immune to energy weapons consumed 60 points of life energy. He only had 40 life energy remaining to assign to attack, speed, HP and agility. His all-round attributes naturally took a big hit.
And of course, Jones' resistance to firearm-type physical weapons had also weakened a considerable extent!
