1) If you don't BSA things can get messy. Many resource makers do not want the file paths and names of their meshes and textures changed. So you cannot pile all your meshes and textures neatly into folders with your mod's name. If you don't BSA you will have a bit of a mess and there is nothing you can do about it as you must adhere to the wishes of the makers of the resources you use. This is the case for my upcoming mod that uses hundreds of resources.
2) If you BSA the files then this can cause a problem because of the limited number of BSA's that can be utilized by the game.
Which is the lesser of two evils here? What are your thoughts and how do you prefer to package your files?
BTW, I started a new thread as the other BSA topic's OP post is not asking this question.
For myself I prefer to not have BSA'd mods as I like to tinker with all the meshes and textures and it is just plain easier. I have had problems extracting files from BSAs.