Counter-arguments ahoy!
Arguably, if something's portrayed exclusively as annoying, it probably is. While outside of D&D gnomes are seen usually as "earth dwellers", and caring deeply for nature, D&D attempted to recast the race, and make them more interesting, particularly for players. Hence we get the idea of Gnome tricksters, to appeal to those who want to play prankster characters. Ultimately, it was decided that Gnomes simply did not appeal enough players, and was removed for that reason.
Halflings have been in D&D since first edition, when they were called hobbits, yes. And yes, they were blatantly copied from Tolkien. However, since then the race of Halflings have been developed to fit with how they are played, and they no longer really resemble Hobbits.
Gnomes may have had the potential to be an awesome race, but they weren't liked. So they have lost whatever potential they might have had. If you can re-fluff Gnomes to improve upon them, feel free. I mean, it can't be hard, 4chan pulled it off with Sergals (but don't tell /b/ that).
And you're knowledge of both LotR and D&D seems lacking. Elves have always been described as attractive, but Tolkien made his tall, while D&D kept theirs short. Tolkien did not create Orcs, but did define their role in most modern fantasy. And as for dwarfs, in Tolkien, and D&D, they are a very serious race. I don't know where you got the comic relief idea from.