Hold up, the Omnitrix only allows Ben to transform into species that are sapient with one of the least intelligent species he can turn into being Wildmutt. It will not scan the DNA of creatures that aren't sapient, it won't let him turn into say a dog or something because a human mind can't handle the feral mind as we learned from the Nemetrix.

So he can at least safely transform into say a Palico and Wyverians since they are at least human levels of sapient as well as any Monsters that are as or more intelligent as say Wildmutt. So he might be able to turn into a Zinogre or Kulu Ya Ku, a creature with enough intelligence to show pride and a bird that can use simply tools respectively.

Not sure how far he could make it since he won't be able to use all of the Monsters in Monster Hunter due to how the Omnitrix works but he would do pretty well, maybe even take down an Elder Dragon or two by turning into the right kind of Monster.

He might also be able to turn into a Monster Hunter assuming that they are genetically different enough from a baseline human, if so he might stand more of a chance in the Monster Hunter universe.