Nobody is asking SE to streamline stuff or to change how they are making quests (actually we could discuss this but that's beside the point). They could just make it so, as an option, the first story quest of the new expansions to be accessible before finishing the MSQ from the previous expansion. And to avoid people who d accidentally take that quest before finishing the previous storyline, they could just add a text disclaimer before you take it if you didn't complete the previous MSQ.
Concerning you're first point, I m puzzled because I don't really know what you're talking about. Nobody is asking to replay stuff or whatever (or that's another issue and beside the topic at hand).
There are no problems, only solutions. The only thing making SE "solving" that issue with boosting potion is pure greed and trying to monetize the tedious aspects of FFXIV. But if we learned something from microtransactions in video games, usually trying to get money out of the tedious aspects of a video game doesn't work. The most successful F2P games are always those in which players are happy to spend money on completely neutral or optional stuff on a gameplay standpoint (see league of legends, as an example).