If anything, I can see why they dumped the characters...already having tough, honest detectives in the GCPD would take away from Gordon's specialness.
Then why set them up in the first place? Or why not at least include a
reason for their departure, like, say, a mention that Commissioner Loeb had them reassigned as a countermove against Gordon? Not only did they abandon the plot thread, they didn't even give a reason for abandoning it. They just forgot about it and expected the audience not to notice amidst all the other random stuff going on.
Let's not forget, Allen and Montoya were set up as significant for Bruce as well as Gordon -- the ones Gordon told Bruce he could turn to if anything happened to him. Given the desperate straits Gordon ended up in later in the season, that's something that
should have been mentioned again, purely as a matter of continuity. Failing that, there should've been an explanation for why they were no longer in the picture.
I see the change as a casualty of FOX giving them six more episodes. The season started with a plan to do an arc in a certain number of episodes, but once it got expanded, they had to stall, to drag things out. Whatever plan they had to show Gordon gradually accruing allies and strengthening his position got postponed -- and then ended up being totally abandoned, with no real progress made by the end of the season. As I may have mentioned before,
LOST had the same problem, its success leading it to spin its wheels and abandon any real progress to its storylines, just using serialization and endless cliffhangers as an excuse to avoid actually advancing the narrative.
I take the viewpoint that you only use characters if you absolutely need to, even if they're series regulars, and if a story moves in a particular direction that doesn't absolutely need some of your major characters, you follow where that story leads and then come back to the characters you'd 'neglected' once there's a story reason to.
But as I said, there were circumstances where they should've at least been mentioned. And really, the abandonment of Montoya and Allen is just a symptom of the larger problem of the abandonment of any arc or progress on the corruption front. The first part of the season had an arc -- Gordon started out a man alone, then he eventually won Bullock over, then he convinced Montoya and Allen he was on their side, then he scored a coup by gaining Essen's support in bringing down Flass. And then in the back half of the season, there was no more progress at all. Sure, they introduced Loeb as Gordon's nemesis and Gordon managed to hold him at bay... but then it just froze there, and the season ended with no resolution of it at all. At the very least, that's an inelegant and awkward plot structure.
For me, Allen and Montoya 'disappearing' part-way through Gotham Season 1 is no different than Bran Stark, Osha, Rickon Stark, Hodor, and Meera Reed 'disappearing' from Game of Thrones Season 5. The writers and showrunners of GoT will bring those characters back in once it's appropriate for them to do so narratively, and, in the meantime, the story operates just fine without them, and I firmly believe that Gotham's showrunners will do the same with Allen and Montoya.
I don't watch that show, so I can't judge the merits of the analogy. But I'd be surprised if we ever saw the return of two characters who disappeared without a word of explanation less than halfway through the season.
