I don't much care for the idea of jury-rigging alien weapons to existing ones, but I am a fan of opening up new ammunition types for existing weapons using alien weaponry. The Kerrblade tree could perhaps lead to a new set of monomolecular fragmentation grenades, then shotgun shells, and finally Monomolecular Sniper/COIL rounds.
From reading the plotline post(s), it seems that the aliens, while significantly advanced technologically than humans, seem not to have considerable experience with battlefield tactics against a capable opponent, and the imagination behind our more specialized, and brutal, weapons. Though PHALANX is starting well behind the curve, it seems that there is plenty of opportunity for them to redesign and overcome the shortcomings of the alien weaponry. Of course, I could see the aliens producing similarly versatile weapons in some cases after seeing what the humans have accomplished, or after capturing some from a botched mission, but this could lead to an interesting arms race and escalation of conflict in the mid- to late-game, an element past X-COM games have lacked to some extent (later in the game the aliens would pull out some nastier toys, but not obviously developed to compete/counter human weapons and tactics).
