I'm playing much more on my R/M side and am just gearing up the mage so it's not an expert opinion but the way I look at this: Shadow Protection works (or: should be used) in a different way on trash/out-of-instance (solo etc.), and in a different way on a boss fight.
1. For solo (trash or out-of-instance) the main thing is fearing attackers and auto-casting Kiss of the Vampire on them - your next two attacks will do tiny bit extra dmg etc. Altogether nice, but absolutely no benefit from the cast-speed buff compared to other mages (you do have +11% if you put your TP in Shadow Protection, but all other mages get +10% from Clear Thought for free).
2. During burn: you will want to cast as fast as possible; you will use Ancient Spirit Water and it's kind of OK-ish that you cannot additionally use long-term Clear Thought or Shadow Protection. But the problem is that you basically have to turn Shadow Protection off (to use Ancient Spirit Water) which also means that you will get almost no perks from your elites (you will still benefit from the second Burst, Miracle etc, but elites themselves will simply not be used...).
3. But: after the burn all other mages cannot use Clear Thought (as it shares CD with ASWater), while M/R can turn Shadow Protection immediately after ASWater finishes. So then you are in the "solo" situation above but indeed you do benefit from the full +11% compared to other mages.
So: it's not completely useless, and it's not a right-out bug.
But M/R is weaker than other mages (I myself am still looking around, but I usually go as M/Wd and not M/R if I want to see my magical side), and it would be nice to see if a small boost could make this class a bit more popular.
Allowing Shadow Protection to stack with Ancient Spirit Water and Clear Thought might be such a small boost, and may be very easy to implement.
1. Allowing Shadow Protection to stack with Clear Thought would make soloing easier.
2. Allowing Shadow Protection to stack with Ancient Spirit Water: during burn you would have Shadow Protection on: no diff for the casting speed ('cause you are at the limit anyway) but it would mean that sometimes Kiss of the Vampire (and associated extra dmg for the next 2 attacks) would also trigger etc. So it might be a small benefit you might actually see on average.
3. After burn: no diff from allowing stacking (both Ancient Spirit Water and Clear Thought are on a shared cooldown, so you have only Shadow Protection, just as it is now).
So even if it is not a bug, it is a nice idea (imho) for a little change (a new feature request if you will) that might make M/R a bit more popular.