In reality, unless you are going into a parish or ministry where they would be asking this question in the process of installing a new instrument, you have to actually 'make do' with what is already there.
When I used to play in churches, half the challenge was how to make full use of the resources at your disposal even if there really wasn't much there to play with. Some of my most rewarding experiences was with smaller instruments or making the best of poorly maintained organs - making a crap organ sound decent or even good.
I think the acoustic of the building can have a bearing on the size of the organ. An instrument with a just a small collection of stops can sound amazing with a good acoustic. I have played large instruments which sound awful in a dead acoustic.
2m Viscount Opera Organ