Thunder has 120 Power, 70 Accuracy, 30% of paralysis, ability to hit Pokemon using fly/bounce and 100 Accuracy in Rain
Blizzard has 120 Power, 70 Accuracy 30% Freeze and 100% Accuracy in hail
Focus Blast has 120 Power, 70 Accuracy and a 10% chance to lower the Sp. Def
As you can see they all are similar but Thunder has the most pros so it's a great question asking why Thunder has so much more PP. Also Focus Blast seems so inferior in terms of effects you'd think that it should have more pp too.
I believe the difference between Thunder and Blizzard was that in Gen I Blizzard was originally a 90 Accuracy with a 10% chance of freeze while Thunder was a 70 Accuracy attack with 10% chance of paralysis - so in Gen I it would make sense why Blizzard would have lower PP then Thunder, due to the difference in Accuracy.
The fact that Focus Blast was introduced in Gen IV could make a difference, since Gamefreak doesn't mess around with the moves too much (There was alot between gens 1-3 but otherwise it stays relatively the same) so Thunder and Blizzard were kept as they were and Focus Blast was given what it is now.
Focus Blast was also brought in to counter the need for a strong Special Attack fighting move - it was introduced with Aura Sphere I believe. In Gen IV, all the strong moves had 5PP, and like I said before GameFreak made next to no changes in the moves apart from giving Thunder, Blizzard and moves like that a chance of hitting through Protect/Detect (30%) in certain weather
Additionally, Thunder has the least distribution out of all the the 3 moves - so you can see sense there why Gamefreak would make it Thunder had more PP.
Yeah thats basically what I think :P