In decreasing order of personal desirability:
Remove party restriction on Prayer of Healing
Why: It's no longer needed. Back in the days when tanks were grouped with Warlocks to get Blood Pact while working on the first iteration of Ragnaros - sure - maybe this made sense. Now, this is the last bastion of an outdated party-based model for healing which is frustrating to coordinate around.
What could make it better: A smart heal! Nothing needs to change (though I suspect we'd see a minor HPS increase from less wasted PoH), and it would work the same as CoH from a target selection perspective. My guess is that this is actually pretty hard to do. WoW's been around for a long time and PoH is one of the oldest spells in the game (both in wall time and spell id enumeration). This considered, organizing groups around the one final spell that has important group restrictions is getting old.
Chakras need more fluidity
Why: There are many times where I'd like to switch stances for a few spells and then switch back to what I was doing before.
What could make it better: Now that some spells have 'charges' (Monk roll most notably), this tech might be well applied to Chakras so we can (at an advanced level of play) stance swap to a minor degree. As a suggestion, 2 charges with a 30 sec. regen sounds fun. That allows us to go 'there and back again', but only every 30 sec.
Apply the concept of Totemic Restoration to Lightwell / Lightspring
Why: The Lightwell CD is particularly annoying when running anything with heavy movement (dungeons, scenarios, PVP) because it will despawn due to range, leaving you with a barely used Lightwell / Lightspring and a long CD.
What could make it better: Totemic Restoration - "When a totem is replaced or destroyed before its duration expires naturally, its cooldown is reduced in proportion to the lost duration, up to a maximum of 50% of the full cooldown."; something along these lines would be nice for LW as well, when despawns occur due to range.