The question of the difference between a speed light vs pop up shooting straight on wasn't answered so I guess it really isn't known IF there is a difference. Don't have a speed light to run that test but thought someone here might know the answer but obviously nobody knows the answer. IMO and it strictly an opinion - it will be be the same level of harshness but the speed light can reach further than a pop up.
This statement is akin to saying that the only difference between a DSLR and P&S camera is that you can change lenses on a DSLR. If you want to try to minimize the differences, then try again. Even with bare, direct flash, the hot shoe flash will look better. It's a larger light source and it's off axis. It is inherently softer light than the tiny pop-up flash. Beyond that, you have more control over the flash, it's easier to add light modifiers, you can bounce it (not just off the ceiling!, try a wall, piece of paper, friends white shirt, just about anything!), if you have a sync cord, you can bring it even further off axis, it won't drain your batteries as fast (since they have their own power), do I need to go on?
You're right, there might be very little difference between an un-diffused hot shoe flash, direct on, and a pop-up flash, but most people don't use their hotshoe flash like this. Stop with the straw man argument!
Forget about whatever diffuser or bounce or whatever is being used to soften the light. Flash is flash with the only differences being how far away from the lens the flash head is and the amount of power the flash can generate. A person standing 10 feet away with a forward firing flash without anything to soften, diffuse or anything else to stop 100% of the light from reaching the subject (trying to be as exact as possible) using the camera's TTL metering should look almost identical with either a pop up or speed light IMO.
There's a third difference that you conveiniently forgot to mention. Size of the light source. Bigger light source = softer light. I don't have my equipment with me at the moment, but the flash head on my 430EXii is at least 7 or 8 times as large as the flash head on my pop-up flash. A large hot shoe flash has inherently softer light than a pop-up flash, given the same distance and flash power.
Straw man again? If it was such a dire situation, I doubt very many people would refuse to shoot in this situation. However, I can pretty much guarentee that a good photographer would still do anything in their power to not have to use the pop-up flash. Adding more light to the scene, cranking ISO, putting on a fast lens, shooting wide open, etc. I'm sure if the pop-up were absolutely needed in this VERY unlikely situation (because, afterall, if it was that important, you wouldn't bring just one strobe, or something for backup, that's just stupid) most people would do what they have to do to get the shot.
I posted a photo using the D90 with it's pop up flash. As I have said, I don't find it bad at all. Is it that the D90 is far superior than the rest of the DSLRs - I doubt it. Would the photo look amazingly better with a top of the line front firing flash unit - I doubt it.
Not to be the bearer of bad news, but that shot really isn't that great. I can assure you that with a hot shoe flash, I could have made it about 10 times better. If all I ever wanted to do was shoot my hot shoe flash un-diffused and direct on, you're right, it would be a waste of money. However, that's the great thing about that piece of equipment, that's not only way, or best way to use it.
As far as shedding a tear - yes I did but it is because people buy expensive items and don't learn how to use them. If someone can master the dreaded pop up flash imagine what that person can do with a real flash unit!
Yes, it's a waste of money to buy a piece of equipment that will make your flash photographs better. By the way, you haven't mastered the use of the pop up flash. And even if you have, you've the proven to me that the $250 I spent on my 430EX II was well worth it, since a non-master of flash (me, apparently) can get better shots with a hot shoe flash than a master of flash (you, apparently) with a pop-up. Assuming of course, that the photo you posted, at least twice now, is showing your masterfulness.