Well the two bedroom suite would get you two private bathrooms, and it would certainly accomodate your family at this point in time based upon the ages of your kids. It would also give you more space to spread out a bit, and allow you to keep better tabs on everyone.

On the other hand it might drive up your costs, and it takes away the independance that you were thinking of giving to your older son. Additionally your four year old might enjoy have a bunk that's her size, not to mention being able to get the top bunk. In a bedroom, I think that safety strap may not allow her to occupy the upper bunk, unless she's very tall for her age. If she's more typical in height, then there is a chance that the strap would not keep her from rolling out of the bunk.

Only you can decide what works best for you and what you are most comfortable with.