I would like to see Inner Will reduce the GCD of instant-cast spells by .5 seconds in addition to its current status. I would be okay if this required a glyph.
I would also like to see Borrowed Time grant 20% spell haste/reduced cast time and stack 2 times.
I would like to see Train of Thought allow Heal, Flash Heal, and Prayer of Healing to reduce the cooldown of Inner Focus instead of being restricted to Greater Heal.
I would like to see Strength of Soul also include Prayer of Healing as a spell that reduces the duration of Weakened Soul.
I think these changes would allow room to nerf Atonement to 50% of dmg done and help to make Disc feel like a full spec instead of a two-hit wonder (Spirit-Shell + Atonement). I think a glyph to reduce the dmg of your Smite, Holy Fire, and Penance by 25% but increase the healing to 100% of dmg done would be suitable.
On a side-note, I would like to see Glyph of Reflective Shield become baseline and a new glyph introduced that would cause PW: Shield cast on other players to also reflect 45% of dmg back to the attacker, and allow these reflected attacks to generate Evangelism stacks.