Been thinking about this as well. The system was problematic in some ways and they changed it but there's still things to be learned from it. The brilliant part was that it gave people choices. If you can pick from any 6 weeklies, but you get the reward after two, that gives the developers leeway to put in more specific weeklies, and players the freedom to pick those that fit into their playstyle. You had group challenges, solo challenges, minigame challenges, jumping puzzle challenges, challenges for the three different game modes in general (pvp, pve, wvw), lots of variety.
Of course you'd have to tweak the numbers and probably introduce more challenges (some archwing-related maybe? people would complain about that in the current system but if it was optional it would be fine), but it would solve most of the problems. Most players would of course just do the ones they feel are "easiest", but those who like to do endurance runs can do that, those who stumbled upon a lot of ayatan statues can fill those, etc and more importantly it gives the option to avoid things they don't like.
You might even - thinking back to GW2 again - introduce PVP challenges if that fits into your design plans.