Generally speaking, RCA cables are lower in ohms, therefore voltage drop and power. However, this can vary widely and is only a generalized statement that is certainly not true for every 3.5mm cable compared to an RCA cable.
The primary difference in connections is that 3.5mm is only appropriate for portable use. Why? Because it's when, not if, that the signal connections fail. There are 1/4" plugs pulled out from attics and musty basements that have been sitting unused for 50 years and they still work. A 3.5mm plug and socket may fail in a few months, depending on the quality. There are real physical limitations with the 3.5mm connection. Spring strength with such a necessarily small piece of metal, corrosion resistance when the contact surface is a few arc degrees of a 3.5mm circle, etc., etc.
I'm not saying there isn't a place for 3.5mm, but if you have a choice and you're not interested in portability, the use of 3.5mm connections is just asking for trouble.