After the negative outcry following Transformers: Revenge of the Fallen, there were several minor creative differences introduced in the third film. Some of these differences were in how the Transformers looked & acted. For instance, many of the racial stereotypes depicted in "Revenge of the Fallen" were toned down considerably for "Dark of the Moon." In addition, several attempts were made to give Decepticon characters additional dialogue & personality. This trend continued with "Age of Extinction", with both Optimus Prime's original truck form (albeit white) and the Dinobots being added largely as fan service.
It's likely that the switch from "home-grown" weapons to actual weapons was simply one of these changes, perhaps in a bid to bring it closer to the source material.
The most reasonable in-universe explanation is that the new weapons were designed by (or with the assistance of) the NEST Team scientists. It's shown that NEST has begun experimenting heavily with Cybertronian technology during the three years between "Revenge of the Fallen" and "Dark Side of the Moon", along with help from the Autobots. It's highly likely that the weapons seen in use by the Transformers were, in fact, a product of these joint efforts.