I know this is late and we have to decent answers already, but them two answers did not pick up on anything that actually justifies using it apart from it being more reliable / more powerful. Also 20% para chance is not a good reason to use it :P
First of as Fondant said Fusion Bolt is the more accurate move. It also usually OHKOs everything it hits super effectively. Now they are two very good points but is going for a reliable move the better option? I think not, and I will tell you why.
Fusion Bolt may OHKO everything it hits super effectively, but who would be dum enough to stay in anyway. Would you keep your Kyogre in on Zekrom? I think not. The only time they would stay in is when they can not afford to switch, the Pokemon is as good as dead and if they need a free switch. They could also over predict and stay in but I doubt anything would fancy taking an Outrage / Dragon Claw anyway.
Now if the opponent does make the switch, unless your running a Choice Band set you will not be hitting to hard. If the opponent switches in a steel type such as Ferrothorn then you are not only getting off very little damage, but you are also just allowing the opponent to set up.
The thing about a Pokemon such as Zekrom is that with its very nice neutral and super effective coverage, it can force many switches. With its amazing ATK stat it can really hurt anything switching in. That said weaker moves like Fusion Bolt will not scare the opponent to much. It preforms a very similar role to Kyogre. Nothing wants to take a max HP Water Spout. So why in that situation would you use Surf or Scald? You would not. Similar to why I would not use Fusion Bolt over Bolt Shot as stuff can afford to switch in on it often.
252+ Atk Choice Band Zekrom Bolt Strike vs. 252 HP / 0 Def Ferrothorn: 153-181 (43.46 - 51.42%) -- 10.94% chance to 2HKO after Stealth Rock
^ That damage calc is actually rather scary. If even Ferrothorn fears it, then who doesn't?
252+ Atk Choice Band Zekrom Fusion Bolt vs. 252 HP / 0 Def Ferrothorn: 118-140 (33.52 - 39.77%) -- 95% chance to 3HKO after Stealth Rock
^ That is the exact same set on the same Ferro just using Fusion Bolt. Both these were done with leftovers factored in (Try it for yourself . Now for the difference in base power (which at first seems small), its surprising to see the massive difference in the battle. This is a Choice Band set and it only just 4HKOs.
For a Pokemon that is meant to be feared with max Atk and CBand, it does not hit very hard. Bolt Strike however is basically an easy guaranteed 3HKO, pushing a 2HKO. There is a reason why Pokemon like Salamence run Fire Blast over Fire Fang. Despite it having no investment in SAtk (and even sometimes a negative nature) it hits much harder than a max Atk Fire Fang ever could because of the base power difference.
The same argument applies for using Hidden Power fighting over Focus Miss. Though HP Fighting does hit all the time why use it if even Pokemon weak to it laugh at its power output. The acc is only a small price to pay. But I am telling you now this loss in power is an even bigger price. You may as well just wrap your Pokemon at bubblerap and then see how threatening they look.
252 SpA Life Orb Gengar Focus Blast vs. 252 HP / 168 SpD Ferrothorn: 260-307 (73.86 - 87.21%) -- guaranteed 2HKO
^ If your failing to OHKO a Pokemon with Focus Blast well... Whats the chance of even 3HKOing it.
252 SpA Life Orb Gengar Hidden Power Fighting vs. 252 HP / 168 SpD Ferrothorn: 153-182 (43.46 - 51.7%) -- guaranteed 3HKO
Going back to the loss in power being a bigger price to pay than the low acc. Bolt Strike's acc isn't even to bad. In fact for a move of such power its freaking amazing. 85 acc is the same as Fire Blast. Fire Blast is always used over any fire move and not only because it is powerful but it is surprisingly reliable. 85 % chance? I quite fancy it. That is almost a 1 in 10 chance of missing.
Now sure missing does suck but when your opponent is forced to switch, you can most of the time afford to miss. You would loose a turn but I would much rather land KO's than not. Damaging everything on the switch is better than not very much.
252+ Atk Zekrom Bolt Strike vs. 4 HP / 0 Def Mewtwo: 283-334 (79.94 - 94.35%) -- 50% chance to OHKO after Stealth Rock
252+ Atk Zekrom Fusion Bolt vs. 4 HP / 0 Def Mewtwo: 219-258 (61.86 - 72.88%) -- guaranteed 2HKO after Stealth Rock
If your not hitting hard enough, you yourself will be punished or forced to switch more which isn't good. The above calcs mean that Mewtwo will get a heavy hit on something on your team (maybe Zekrom) if you don't land the kos. After several switch in on rocks, Fusion Bolt only just kills. That's not good enough. Can you afford to be taking heavy hits yourself? I think not.
This answer was to long :L
I respect peoples opinions but as probably the most experience Ubers player on the site, I think its fair to say that paired with the above points, nothing can really justify using Fusion Bolt over Bolt Strike. Especially if the points are it has a 20% para chance xD(If your worried about acc, its not to bad but running both is not a bad option on a choice set).
I agree with Jofly use Bolt Strike
