Playing Super Robot Wars: Original Generation 2 all over again has made me remember something very distinct about the game: the story scenes are very, very long. At the beginning of every chapter you are likely going to read through possibly fifteen minutes or more of character dialogue, and there will be about that much after the battle is complete. I think having that much dialogue is a good thing, since it provides a lot of good story exposition and leads to a surprising amount of character development for the game's large cast, but having to sit through incredibly long story scenes in which multiple different plot threads are unraveling at the same time can get tiring. In a way, I think the game's story is not paired up well with the way the story is being presented.
A part of the problem is that, other than plot events in the battles themselves, the game strictly follows the loop of Intermission, Story Scene, Battle, Story Scene, Intermission. Every story event has to be placed within that linear flow, including everything from conversations between various minor villains regarding their political aims, to discussion of the next mission, to minor humorous exchanges between some of the main characters. Because permanent saves can only be made at the Intermission screen, this means that you need to sit through a lot of dialogue every time you start a battle or end one (the ability to skip through dialogue quickly with a button press helps this, but it is not necessarily the best way to solve the problem).
One way to fix some of the annoyances of this system would be to move a lot of the dialogue from the story scenes to the Intermission phase, where you can still save the game. This is pretty much the approach that recent Fire Emblem games and the Front Mission games take, with the Base system from the former and the interactive first-person perspective of the latter. By chopping up the story into smaller bits and putting them in a place where story changes to your line-up (like SRW route splits) can accounted for and the game can be saved, it makes the game experience less tiring for the player. In this case, the sequence is closer to Intermission, Story, Intermission, Story, Battle, Story, Intermission.
I suppose, though, that as long as a game is ordered as simply a sequence of battles the problem of story pacing seen in SRW:OG2 will never be completely gone. Things like long story sequences describing the villain's goals which are completely unrelated to any individual battle are necessary to a good story, but tend to bog down the story flow surrounding an individual battle, and this can;t be easily avoided simply by shifting when you can save. That said, I think some other games in the genre, like Final Fantasy Tactics, manage to escape that limitation. In that game's case, it does so by eliminating a strict link between story scenes and battles. In FFT, it is possible to fight battles that have very little to no story, and to encounter story sequences that have no battle associated with them. You may have several story sequences or brief inteludes focusing on a villain for a while, and then get into a sequence of battles in which the story only focuses upon the direct cause and effect of each battle. Character development of the main cast in FFT can be a little thin, but other than that the dynamic pace of story leads to it flowing well.