From your posts, I guess your wife is an emotional person. And, four years is a long time. I understand where your wife is coming from in her wanting to be with her mom asap. They've got a strong mother-daughter connection
The Manila visa office is one of the few visa offices that considers the family emotional aspects in visa applications. I recommend submitting a paper application. Don't apply online.
Also, the joint invitation letter co-signed by your wife and yourself must have a bit of an emotional touch to it and mention why your wife wants to spend quality time with her mom. Don't make it too teary though LOL. And, please don't mention about your future babies
If she's applying for a super visa then mention a stay of 8-9 months. Just maybe her mom will agree to staying longer