Currently, the champion system is working well for one reason:
There is a limit on the amount of champion points available to spend thus creating build diversity, which is what is intended.
However, over time as this cap rises it'll be easier to see where you don't need to invest. If the cap ever hits 3600, any player with 3600 points in combat with another max CP player would be fighting as if the Champion System didn't even exist. On top of this, most people's builds will be completed long before hitting even 3000 CP due to ineffective or useless passives.
Any stamina player wearing 5 pieces of medium armour can instantly ignore both Light armour and heavy armour focus in the warrior constellations, can potentially ignore both Magician and Arcanist in the thief constellations and will most likely ignore the entire Apprentice constellation as well as Staff Expert under the Atronach in the mage constellations.
Furthermore, currently some passives have similar effects but some are performing better than others which make them unfavourable while the cap stays low. (Elemental Defender + Hardy are much better options than Spell Shield or Armour Focus).
To make this system still as good as it is currently I think we should group certain passives together to free up more stars for additional USEFUL passives, so that if a greater cap is set in future it is still a struggle to decide what passives you need and what ones you don't. Obvious suggestions for this would be to group all 3 Armour Focus stars in to 1, group Precise Strikes and Elfborn together, group Warlord and Magician together and maybe group Arcanist and Mooncalf together. Passives like Shade are borderline useless due to skill point passives and should be changed to something more useful also.
I can't think of anything to suggest in place of the passives if they ever were grouped or removed but something along the lines of an increase/decrease in damge dealt/recieved by AoE abilities might be a good starting point.
I'm interested to see what other people think about this idea.
XBOX GT: InFernal Entity
Zoarava the Dark Reaper - Level 50 Khajiit Stamblade
Valyria Uviryoni - Level 50 Dunmer mDK Vampire
Pale Shade - Level 50 Argonian NB crafter