I think they suffered content cuts that they became filler characters. (actually most new human characters on Normandy are just fillers)
Allers could have been wonderful if you actually get to see her interviews at Citadel (like, you get to see clips of the Normandy crew's interviews or reruns of Shepard's interviews or clips of the situation on earth or clips of VS's Spectre ceremony). Instead, we get a nondescript guy and a woman in the background. I like listening to the ANN news but I think that's an oversight on Bioware's part. She could have been more interactive if they actually let her be.
As for James, the comics and the movie fills in much of his back story. If you play the game alone, he does feel unfinished and bland. Its sucks that they didn't make him romanceable since romance content does add a lot of depth and characterizations. I think he's pretty terrific and interesting as a bisexual option (even better than Kaidan's) and there's continuity to this as he has a big crush on Shepard for years (Paragon Lost).
Honestly, I like to think that he's a substitute-Ashley. Nobody really explain how she get from Operations Chief to Lieutenant Commander in more/less than a year but I think ME3 did better fixing this rank thingy with James. I don't think we're made aware that Lieutenant James Vega was is in fact Lieutenant Commander Vega (Paragon Lost). But he turned down his promotion because he didn't feel like he deserved it after Fehl Prime and he suffered some period of existential crisis (ME: Conviction). It was Anderson who offered him the job to guard Shepard on earth and I do think it was him who recommended James for the ICT program. For all intent and purposes, his story in ME3 is really about his personal journey of self-discovery. Even at the end, he was seen being in command over a group of soldier so I'm not that far off in this.