It did always seem strange to stick Moltres in the middle of a dungeon that was actually important for progress, unlike Articuno and Zapdos (you could just bypass the Seafoam Islands via Pallet, and the Power Plant served no real purpose other than to hold Zapdos). It does seem like there probably wasn't anywhere else to put Moltres, and perhaps the game's creators didn't want to create another dungeon or anything like that. Still, I wasn't happy when they moved Moltres in FR/LG, I guess because I wanted the games to stay true to the originals in that regard (and do more with the Sevii Islands in other ways).
Moltres generally came so late in the game that I never bothered to use it. On my first playthrough, I had a hard time navigating Victory Road, so I never found it. On subsequent plays, I just didn't feel like it was worth the effort of hunting it down until later.