Yes, in MY OPINION, Bethesda did a piss poor job on some of the guild and civil war questlines in the game.
EG It would not have taken any time at all for them to explain to me that the former Jarl of Riften that I had a great relationship with and who made me Thane would NOW BE DISMISSED because I sided with the imperials and the person I HATED (Maven Blackbriar) would be put on the throne. That is a terrible instance where something that I didn't want or know would happen and was not explained to me prior and I had no way to stop it or fix it after it happened. I can't stand that in a "choose your own path open world game". At least let me kill Maven afterwards or remove her from power. The game should know that I despise her and was good friends with the old Jarl.
Tullius says that Maven Blackbriar will take the Jarldom as soon as negotiations are finalized in that discussion.
Yes, she already pretty much ran things, which is evident from the very first Thieves Guild missions.
An outcome that you
don't like is not the same as bad writing or poor quests. Choose your own path/sandbox games do not mean that you get everything you want exactly the way you want. Actions have consequences. Sometimes, they're consequences that we don't particularly care for.
All of that said, if you haven't done the Civil War quests, your character could use this as their reason for going Stormcloak. He/she hadn't realized Maven Blackbriar would be given control of Riften, finds Blackbriar utterly despicable and can't believe the Empire would put someone like that in charge while deposing the Jarl you were fond of, etc, so viva la revolution.
...Of course, that might also result in a few Jarls you're fond of in other places being replaced. Such is life.