Now let's see here...
In a neutral battlefield, there would be enough space for the enderdragon to freely move, and she would also lack the ender crystals since that only spawns in the end.
The Wall of Flesh is huge, and targeting the eyes and mouth is an obvious thing to do, even for something with animalistic behavior. Not that this needs to be pointed out, since the Ender Dragon already has non-physical interaction and could very much attack the Wall of Flesh anywhere she wanted to.
Ironically, this intangibility argument was brought up for Wall of Flesh, but no one brought up the Ender Dragon's intangibility either. (But to be fair, I honestly think the Ender Dragon's intangibility is game mechanics so that it doesn't destroy The End while players battle it, so I won't use it as an argument).
Nothing says the Hungry could pull the ender dragon like it can the Terrarian. Just eyeballing the ender dragon puts it at several tons, the Terrarian likely wouldnt weigh any more than 500 lbs, and that's a generous weight by including the equipment.
The difference in AP is only 1.19, so while an advantage, it's not a major advantage for the Wall of Flesh. To give a better idea to think of it, if the Ender Dragon was 100 joules, the WoF would be 119 joules. Not a big difference.
Both characters have equal range opportunities. The lasers are quick, so the Wall of Flesh could easily shoot the dragon in motion, and while the Ender Dragon's acid blasts are relatively slower, the Wall of Flesh is such a huge target that it's damn near impossible for the Ender Dragon to miss.
Honestly I would have said this battle would have likely been inconclusive if it weren't for the fact that the Ender Dragon had acid attacks, which the Wall of Flesh doesn't resist, while also being, well.. a wall of flesh.
So I'll give it to the Ender Dragon for her constantly spamming acid, which should severely weaken the Wall of Flesh very quickly.
Edited over an hour later: this might turn into a full on stomp after I
recently posted an upgrade thread for the ender dragon calc .