I presume this is at lvl 50 but against what levels of mobs and how are your powers slotted. Remember nova form has a huge acc bonus so you can easily run those powers slotted for recharge or debuff instead of accuracy and this may give a greater bonus to nova against +3/4 mobs or against bosses/EB/AV. Of course it is possible to run tactics in human form as well which may partially offset this.
Mind of Gaia lvl 50 Defiant's first Mind/Storm 'troller.
Deadly Doc 50 Dark/Dark Corr
and lots more on Pinnacle,Union and Defiant
The City of Data figures are all for level 50 and even level mobs. My figures assume every attack is 3 slotted for damage.
Basically I'd seen a lot of people saying that either Nova or Human form gave better damage and decided to see for myself as there was no real evidence either way. The above is the theoretical total damage based on my build (and I do have recred slotted in most human attacks and both Nova AoE) and one or two assumptions (such as how Build Up is used). Of course slightly different slotting will change the results but this was only supposed to be a basic comparison.
As you say, there are other factors like acc that will also come into play. Nova form may lag slightly in single target damage but it's To Hit bonus means it should miss less, especially against higher level foes as you point out.
Like I said tho, this is only a rough comparrison. 
I can´t say that I am in any way surprised by the result. It is no secret that the nova form is better at AoE damage while the human form has some hard-hitting single target attacks (and a mob size of 3 is typically the point where AoE starts to be better).
So, depending on a player´s preferences of playstyle and solo-/teamplay he might get the impression that the one or the other gave them better damage numbers. Well, at least the human form´s single target damage is something special for Kheldians... unlike the nova form´s AoE damage which is completely outshined by the Purple Flying Fortress of Doom that is the fully buffed WS nova.
If it has eyes, you can blind it, if it has blood, you can make it bleed, if it has a mouth, you can make it scream.
cool post Faultline!
@ExtraGonk
So for somone new to Pb's (ie me) I should be using Nova for AoE, human for ST damage, this is what I had planned anyway, to make the Human into more of a Blapper
Hawk
Following on from another thread which went off on a slight tangent, I did a little rough and ready testing on which gives better damage for a PB - human or nova form. Rather than trying to find the most efficient attack chain I just went and hit a GM for as long as I could stay alive and then checked how many times I'd used each power. I thought this might give a slightly more realistic idea of damage done in an actual fight rather than theoretical damage. Plus I was too lazy to work out an attack chain.
After that I used the figures from City of Data to work out total damage over a given period of time. Keep in mind that this is for my build - ie running hasten and with redrec slotted in various powers. It's only supposed to provide a basic comparison. All damage figures are for a one minute period, 3 slotted with damage SOs with build up used (but only for the first volley with Nova). Human attacks were GE, GB, IS, RS and SF, all four Nova blasts used.
Single target, no build up
Human - 3890
Nova - 3735
Single Target, with build up
Human - 4390
Nova - 3874
Single target with build up and Cosmic balance from 3 team-mates
Human - 5575
Nova - 3874
As above but against 3 mobs
Human - 7115
Nova - 8307
With 8 mobs
Human - 10966
Nova - 19388
15 mobs
Human - 16357
Nova - 34903
15 mobs and you happen to team with 6 defenders and a tank
Human - 20922
Nova - 34903
As above but single target
Human - 7155
Nova - 3874
Enough figures I think. I believe they are correct but I don't claim to be as good as Dr Rock at this sort of thing.
It appears nova can hold it's own against a single target as long as there is no cosmic balance to help human form. Once spawn size reaches about three, Nova pulls ahead in total damage and keeps increasing it's lead the larger the spawns get. Photons would help both single and AoE damage for human form but are not reliable or up very often to factor in easily. The knockback on SF may actually lower the DPS slightly due to having to run around more chasing mobs. A human blapper using the two AoE blast may fair better in AoE damage but will probably have to drop (or not use) other attacks to make room in the chain, lowering total damage anyway.
Ok, I need some brekkie now.