Gentlemen.... behold!
Are you ready to rock!?
Well actually, I pulled up Manly's gear and did a lot of testing in magegraf. I fixed the coefficient, put in the new AM glyph, nerfed the timer stacking, etc. What I came up with was very interesting. There are a couple of ways to play arcane spec, mainly, an easy way and a best way.
Rotations
First I tried fixing the rotation at ABx3 AM. Now, using this, each time you use Arcane Missiles there's a 49% chance that the AM will be affected by Missile Barrage. Hmmm.
Next I tried a rotation of ABx3 ABr, but the ABr would be substituted for an Arcane Missiles if MBr was active. So you figure about half the time its using Missile Barrage, the other half it's using ABr. This ended up being MUCH stronger, 100-200 dps at least.
The napkin math on this difference is deceptively simple. Compare the dps of ABx3 AM and ABx3 ABr assuming no MBr procs. Find the total damage of the cycle, divide by the total time, and you have the dps output. Without MBr, an ABr as finisher is slightly better. The same comparison can be made with MBr active, you simply double the AM dps, and in that case of course AM is way better. So the switch-up depending on procs is always valuable. The chance of wasting an MBr proc, due to it occuring on your third Blast but not on the first two, is only 12.8%; not nearly enough to make a set rotation viable.
So what we know for certain is that when doing a rotation of AB and a finishing spell, Arcane Barrage or Arcane Missiles, it is always best to adapt your finishing spell based on the presence of MBr procs.
Now, I wanted to see if it was better to adapt to MBr procs by burning them on the next spell, instead of finishing the rotation. This one is a little trickier, and I essentially had to rely on magegraf's somewhat random spread of procs over a long duration. There are two key advantages to burning a proc immediately. The first is that you create the opportunity for more procs, and the second is that you save mana. The first advantage appeared to be negligible, as magegraf reported a 5 dps loss (seriously) from responding to MBr procs. The second advantage, however, was noticeable, as you do save a decent amount of mana by not going the full 3 AB stacks when you can avoid it. This leads me to believe that there is definitely incentive to respond immediately to MBr procs, but it isn't a crucial part of playing the spec and may be subject to more scrutiny.
Glyphs/Armors
I tried various different combinations of glyph/armor relating to mana consumption. Firstly, glyph of mana gem is still inferior to glyph of mage armor (if you are using mage armor, obviously). Secondly, at 300 seconds arcane was still able to maintain an ABx3 + finisher rotation without significant mana issues while using Molten Armor. This produced the best results by about 50 dps. However, depending on your gear, circumstances, etc. your mileage may vary. If you can't maintain an ABx3 cycle, it's probably better to stick with a mage armor/glyph setup. Magegraf can help you with this decision, of course.
The other glyphs used were Arcane Missiles and Arcane Blast, I did not bother testing with substitutes as these seem very obvious.
Final Verdict
I also changed the default fire setting to use Molten Armor instead of Mage. Aha. Fireball beat out arcane by about 30 dps. Effectively, I would say they are dead even. Poor frostfire and frost are sitting a good deal behind now that their mana advantage is useless.