Yep, have run into the same exact problems you're outlining here. I use my best 12 on Hard/Brutal, and then I'm scraping a bit on Normal. On the easier (read: non Wrath) weeks, it's not so bad. I don't really want to take up dupes or fringe Hydra champions at the cost of getting masteries on Arena champs just in the hopes of making this go easier.
Getting the quest three times in a week was not ideal. I don't mind passing up energy and such at this stage of the game and have outright skipped the quest a few times now because I just can't be bothered.
See my comment to HQ... 😆