Cotton thread does lose strength over time and also when exposed to direct sunlight. You may be able to unravel some off the spool or cone and deeper down on the spool or cone it may be stronger. It isn't unusual for the same brand of thread to perform differently. The dyes also can affect the thread's strength and performance. Finally it is not unheard of that a manufacturer occasionally puts out a batch of bad thread.
Regarding preference... I quilt on a LA and I really dislike all the lint build up from cotton thread running through such a high speed machine. Inevitably, whenever I use cotton I end up with a lint blob in my bobbin case which throws off my tension. Some cottons are much worse than others. I still use cotton especially when I want a matte finish thread or need a color I can only seem to find in cotton, but I much prefer polyester for ease of use and lack of lint and I really like the shiny finish of many poly's that are marketed as embroidery thread. My go to thread is Filtec Glide but I also use many other brands and types. It all depends on the application. I will often use many different threads in one quilt.