I guess I'm not an typical mage then but I have to agree with some things you have said. However, the example above is Ice-Fire (not Ice-Lightning), so it's not an AoE fusion. You have to pick targets one by one and damage decreases as you lose charges.
Let's just say we are using Fire-Lightning with the damage you just used as an example. I don't know if you took this into account, but the max number of targets decreases as you lose a charge with this type of fusion. So that would be a total of 5+4+3+2+1 (15) total hits. Anyways, you said damage would add up to 20400 if all charges crit, but let's be realistic and just say they crit 30% of the time. According to this number your average is either a) 544 (15 hits) or b) 1612 (5 targets). Anyhow, the total damage is 8160 non crit. If we assume damage crits 30% of the time then, 6120 (8160*0.3*2.5) crit damage and 5712 (8160*0.7) for a total damage of 11832.
I think you're not comparing Thunder fairly.
Thunder would need more than 5 targets to match that damage. And because of the crit rate, it'd probably still do less.
Thunder would need at least 3 targets with equal amount of crits to match.
Since we're doing fusion calculations for 5 targets, then it would be fair if we did the same for Thunder.
Assuming Thunder hits 400 (I don't know your exact Int but I'm sure it's high) on 5 targets, with 3 charges the total damage would be 400*3*5 6000 (almost as much as your Ice-Lightning example, only that no Int factor and just 3 charges!), so if we assume Thunder would crit 30% of the time then, 4500 (6000*0.3*2.5) + 4200 (6000*07) which totals 10200, assuming you have at least 400 Int, damage would be increased by 20%... so that's 12240 damage right there.
A 3 charge Thunder would take 10.5 seconds to load; a 5 charge Ice-Lightning would take 15 seconds (correct me if I'm wrong but I'm not sure if bolts load simultaneously or if both charging speeds are added, 1.5 seconds for each bolt). So on average each fused bolt is 0.5 seconds faster than Thunder... that's a 2.5 seconds difference for a FULL charge, which would totally destroy bolts in terms of damage.
I could run the same calculations if all charges crit but the outcome would be the same since I would have to do the same for both Thunder and Bolt Fusion, and upgrade stones, Int, etc. would have no impact on the resulting number because they are constants and they compound so they can be canceled out. Raw numbers are more important.
However, I would have to agree that things to consider are 1) Casting Speed, 2) Mana efficiency*, 3) Possibility of walking with bolts charged (but they would vanish after 15 seconds if you don't mod), so it would be really stupid to say they wouldn't help to some extent. Casting Speed is a plus but I still think Thunder would be superior in terms of dps. Again, it's situational because there are situations where Fused Bolts would suit better but generally speaking Inter Magic is more efficient and more reliable, particularly against hard mobs. And the max number of targets for Bolt Fusion is 5, while Thunder's is 16 I believe.
*I don't really care about this. I don't even wear a reduction set because I prefer a heavy armor with pd's and high def and prot (enchants+upgrades). 10% mana cost reduction is not that much.