It wasn't supposed to be subtle. Hellboy2 certainly doesn't have the blink-and-you-miss-it nuances that Pan's had, and it doesn't set out to. Del Toro was obviously taking the side of the monsters in this particular show. The plant elemental being a dichotomy of destruction and beauty, the troll market showing that even in a place where brutal instruments and creatures are everywhere, there is a sort of chaotic calm and order, until encroached upon by denizens of our world. The troll market doesn't just emphasise that earlier point, but also shows that various species, be it those two headed gossipmongers or the tentacled Spongebobs, can co-exist peacefully (as peacefully as they can), while humanity isn't even at peace with itself, much less other species and the planet in general.
Nuada's rather poignant phrase is pointed as well :"We die, and the world is poorer for it". Del Toro was obvious in showing that even in violence, Nuada and all the magical creatures were sympathetic, and that in the abovementioned scene, Hellboy and Abe acted more human than ANY of the other portrayed humans. Simple, yet poignant. For those who read more into films, the above line that I quoted can probably be taken to not just extend to magical creatures, but all forms of irreconcilable differences (racism, for example, encapsulated in the talk show about inter-species marriage), and can even be extrapolated to the imaginary.
Hellboy2 isn't good because it is beautiful (which it is). It is good because under all the action and creature designs was a simple, character-driven plot that never overstated its hand or overstayed its welcome, and while sounding run-of-the-mill, is achieved by surprisingly few movies. It is great because it doesn't just tell us what the flaws of humanity are, it shows us these flaws by placing them in contrast to what Hellboy (and Abe/Liz, to a lesser extent) does right, even though he is so much closer to the monsters than to humanity -- he was much more human than humanity itself.