I think this seems to be a curse that almost every TV series is facing right now. Even for runaway critical and popular successes from companies with loads of funding (Thinking Wednesday from Netflix, all the Star Trek shows from Paramount-CBS, countless animated projects from HBO-Max-Whatever-they're-called-this-week) they seem unable to just commit to a production pipeline, everything ends up stalling, and it prevents the kind of success that the production companies wanted, all but ensuring they fail to meet expectations, as multi-year long waits for follow ups means that only the core fan group is going to want to follow up.
I don't know how you solve that, other than grabbing the executives by the shoulders and shaking them until they realise it's nonsense behaviour.
This bugged me as well. I was very surprised in the last ep and the beginning of this one to see just how protective and loving Doctor and Belinda were being to poppy. But then by the end, only Belinda is the one that seems to care deeply for the child. The doctor is given a chance to make a farewell, but then he just leaves with (as I understood it) the implication that he is never going to come back and that he's been replaced by a human dad. It just confuses me why any of that needed to happen.