Thanks for your input. I am hoping someone will contribute to some of the positives of the semi waterproof panniers so I can make an educated decision between the two, unless there aren't any positives. 
Well since I have used both. I'll take a stab at that.
The rain covers are usually a high visibility color which is a plus. They are generally adequate for keeping stuff dry, but you may want to double bag using either ziplocs or trash compactor bags.
The other advantage or disadvantage that comes to my mind is that they tend to have pockets and maybe divided compartments. To me that is a minus because I like the one big compartment approach and organize my stuff with ziplocs. If you like pockets that might be a plus for you. It is personal preference. I thought I would like having multiple pockets, but in practice it didn't work out as well for me.
I find that for a particular listed volume the ones with pockets and multiple compartments tend to hold a bit less since you are likely to just have an item or two in a pocket rather than having it full. I don't think that is a big plus or minus, but might be something to consider when picking the size you buy.
Also I think the ones with multiple pockets tend to be a bit heavier, but that varies some from brand to brand. Some are a lot heavier others less so.