Scramble City takes place between Season 2 and the movie. Of course, Scramble City is crap (nothing more than a half hour toy advert). But yeah, a story that substantially fleshes out that period would be neat. But such a story could be limited in terms of character choices and designs, for instance you might be obliged to introduce characters like Ultra Magnus, Springer, Arcee etc. and they would need to look fairly G1-accurate too. And there would be limits in terms of story direction and not messing up either the past (pre-movie G1) or the future (movie and beyond).

With a story that is set in say the late Autobot-Decepticon War you have far greater freedom with character choices, designs and story direction/continuity. We know basically nothing about how the Great War ended - all we know is that the Autobots ultimately won and the Decepticons surrendered with the signing of the Pax Cybertronia treatise. You would need to introduce Rodimus (and optionally Springer and Arcee too), but that wouldn't be hard and they don't have to look like their G1 counterparts - although the Wreckers story illustrated them appearing as they did in G1 the new line could easily retcon that. Telling stories of ancient Cybertron would also lend greater freedom for story telling but more limiting in toy/marketing designs because of lack of realistic Earth modes.