If you want stronger coffee (referring specifically to the amount of total dissolved solids), then you really just need a stronger coffee to water ratio. Or just simply add more coffee.
Although what I think you are really experiencing is a difference in mouth feel. Using a paper filter with certainly give the coffee clarity. Really fine paper filters (like a chemex filter - being thick and made from soft woods) will evidently filter out very small particles - which results in a very delicate, crisp, and light mouth feel tasting cup of coffee. On the opposite end of the spectrum you have the french press. Which you end up having tiny fine particles left in your end cup, which gives a great amount of body, and a very heavy mouth feel. Both are totally fine cups of coffee, but are totally subjective to your palate.
The thing about extraction is that you really only want to extract about 20% of the coffee you have. If you look at an extraction versus time graphed out, you can see that it represents the curve y=sqrt(x), where extraction continues to increase as time goes on, but at a slower and slower rate. All this means is that by simply letting your coffee brew longer, you are not exactly going to make it any stronger past a certain point. You simply just need to add more coffee. As for the filter - your over all brew strength, or total dissolved solids - should basically be the exact same compared to if you didn't filter it with paper. The main difference is how it's being presented to your mouth.
I think a good starting place is a 1:16 ratio, meaning 1 parts coffee to 16 parts water. Depending on how that taste to you, just manipulate it until desired. Hopefully this helps out!