No issue with toilets in bathrooms and a second toilet is a benefit in my book. We have two bed with one toilet in the one bathroom - we often have overseas visitors an extra toilet would be great - especially when little ones just have to go right now! I would choose a place with two toilets but with shower over bath over one with only one toilet but separate shower if everything else was the same. Three bedrooms sounds like somewhere a family would rent so I think second toilet definitely a benefit (especially if is a big 3 bed - as opposed to a 2 + boxroom type). But to be honest there is never only one thing that is different between two places and I would still rent a place with one toilet, and even if toilet is in bathroom - if the rest of the place is good. Also really the rental market is so strong you won't have a problem whichever way you decide so I would do whatever suits you.