A slight modification to the traditonal VD Pen setup gives about 33% more damage?
Putting the lack of auto targeting on DD aside, I think you're massively underestimating the single target damage of VD.
I made a spreadsheet of the damage per cast at level 20 of all spammable skills, and even without the enchant, VD comes out at 2005.5, whereas DD only has 1039.35. If you take the base as one cast every two triggers, casting every trigger means a multiplier of 2 and two support gems at 50% more damage each mean a multiplier of 2.25. This means the main damage spell will have a damage multiplier of 4.5, while the other has a multiplier of 1. Now if we swap in the numbers I mentioned earlier (assuming the level scaling is the same, but even if it isn't, I doubt that neglecting it makes a significant difference) and assuming there are sufficient corpses, we have ~10k damage per cycle with VD as a main spell and ~6.5k with DD. It's fairly obvious from this that if you don't bother with Bodyswap and can't sustain corpses for VD if you alternate in your Unearth setup, that you just stop alternating and have 9k damage per cycle without DD. If you want to keep Bodyswap and dps, more projectiles are the way to go. 

" Such discrepancy can not exist. GGG would not be that stupid to let such a blatant imbalance exists. Okay, I don't know how you did your calculation, but the damage of VD vs DD is really easy to calculate. I was just a bit lazy to type it out, but for the sake of the argument, I will do it now. So, VD deals: 535 to 802 fire damage at max level (20) > it deals on average (802+535)/2=668.5 fire damage. In addition to that we need to know the bone archer corpse life, which from this thread https://www.reddit.com/r/pathofexile/comments/7r0wun/unearth_experimentation_level_91_corpses_have/ : A level 20 Unearth has level 80 corpse, which presumably has: 16517 life. So VD deals in total: 668.5+ 3%*16517=1164 base damage per ball. We have 3 balls, so there are: VD deals 1164*3=3492 fire damage per cast About DD: I guess I don't need to explain the same calculation, u guess it. I just write down the formula here: (823+1235)/2 + 6%*16517=2020.2 So to sum it up: DD deals 2020.2 fire damage per cast vs VD deals 3492 fire damage per cast So DD deals 57% damage of VD. Ah ha now that I write this (Yes I calculate it as I write), I think GGG is a bit dense in balancing the 2 skills. But hold on! I still have a backup weapon weapon in my argument though. You haven't won yet ! At the time I write this, a VD helmet enchant on Indigon costs around 100120 exalts, so it is pretty much unobtainable. But, you can take a look at my Templar Delve character, I just bought an Indigon Helmet with DD enchant for 30 chaos. So the DD enchant is: " So this is just 45% chance to deal double the Damage, which is just a 45% more damage multiplier. So DD with this enchant deals: 2020.2*1.45=2929 fire damage compared to 3492 fire damage, which is 84% of VD. But, one caveat here, if DD actually uses one additional corpse, we actually don't have enough corpse for VD in the second pen! So, I accommodate this by scrapping VD in the second pen algother and throwing in Cremation. Now let's calculate the total damage: Let the damage of VD /cast=y, assuming as usual every support gems in the main link has 0.5 more multiplier. So we have: y*1.5*1.5=2.25y damage / cast for the usual setup Detonate Dead: 0.84*1.5*1.5*y=1.89y damage /cast Cremation: Explosion damage: 660.68. Linked with GMP makes it: 449 Damage/ Explosion, added per second cast of DD. So this is an added 225 fire damage per DD cast. This means, without considering projectiles part from Cremation, we deal: 1.89y+ 225/3492 * y=1.89y+0.06y= 1.95y Projectiles damage: Well, this is very hard to calculate, but I will take a very conservative approach here: Because it is linked with GMP, it fires 84 projetiles over 8 duration. So it fires 84/8=10.5 projectiles /sec. Now assuming since there are 4 directions: north, ease, south, west, the boss will be hit by 10.5/4=2.625 projectiles/sec. There are 3 Cremation, so this equates to: 2.625*3=7.875 projectiles/sec. We cast around 4 DD casts per sec, so this is equivalent to 7.875/4= 2 projectiles/ DD cast (1.96 round up a bit). What this means is that we deal: (535357)/2 dam /projectiles * 2 projectiles * 0.74 from GMP = 66 damage added for DD/ cast. which is another 66/3492=0.02 y, or we have now in total 1.95+0.02=1.97y Okay, unless I'm missing something, DD loses because of badly balanced number from GGG. Please GGG, do the math before releasing the skills, you can't leave a skill just simply deal 0.57 damage of another skill with better targeting like this !  
Actually, maybe the balls damage doesn't include the % corpse explosion damage. Balls explosion != Corpse Explosion. And the % corpse explosion damage does not actually benefit from spell damage modifier. So for Indigon builds, VD and DD may not be the best choice of spell for damage. I will try to calculate the number for other spell combos.
 
I did indeed not consider the nonspell damage scalable part of the skills, because spell damage is what almost all builds will scale primarily. Pain Attunement, Arcane Surge, RF, VaalRF, even if you don't use Indigon.
And yes, the corpse explosion damage only occurs around the corpse, even for VD, but since the corpse needs to be in range for DD to deal damage at all, this can actually be neglected. Other than that, only Ball Lightning and Firestorm beat VD in single target damage per cast and both need 3 seconds or more to apply their damage at full potential. Because they are also rather limited in the area of application compared to VD which has a homing property, they don't really compete. Discounting Flame Surge which has a rather small range and AoE and requires the enemy to be burning, Arc comes in as a far second with about 60% of the single target damage (with enchant) of VD (without enchant). The advantage is that it doesn't require corpse generation, so if you could use two, you would have slightly higher damage than VD, though less than VD has with the enchant. It's also auto targeting in a smaller range than VD, which is one of the reasons it's in the top 6 skills this league. It does considerable damage if you manage to shock for full effect (still less than VD). After Arc, there's Fireball, which has a decent base damage, but poor targeting profile and is more useful for ignite builds. And at the 7th position for damage per cast, under the condition that it hits an enemy twice, is Glacial Cascade, which has a good AoE profile for mines, but not so good for Poet's Pen. It's another of the few skills that make it beyond the 1% usage, although it doesn't make it into the top 7. Because there's no real skill to pair with Arc, and its damage considerably trails off over chains, VD is the undisputed champion for Poet's Pens. Another take at actually scaling damage off corpse HP can be found here, but it doesn't use Poet's Pens, or Detonate Dead for that matter. 
