Reliance on DI: I hate this part too, DI in essence is very fucked up buff as when all other "single type" buffs were removed DI got added and Focus Magic stayed, either remove DI and buff SP by some margin or make DI raidwide.
Shadow Mastery: Truth to be told I love current shadow mastery, I don't see reason to change it scaling with Archangel would probably just lead to some fucked up full mastery specs involving only mind spike.
Shadow Orbs and Mana: I never ever have mana issues on any of fights unless it's Ragnaros Heroic and even then it happens extremely rarely, as long as you utilize your tools good, you shouldn't struggle with mana.
My problems which in my opinion are much more acute is SW
backlash, now that content is on farm and we are killing everything before AoE burn us down it's not exactly issue but during start of firelands getting 70k backlashes from double crits did make life complicated, add to backlash scaling with damage buffs and debuffs increasing damage taken make this very annoying mechanic.
Other problem is Shadow Orb and their a tad RNG way of proccing, adding a simple cooldown to Shadow Tree which would grant let's say 3 orbs and 5 stacks of evangelism on 2 minute cooldown would be great hell 1 orb on 5min cooldown would be enough just for those fights where you just ain't getting shadow orb with trinkets and power torrent procced.