They don't use the same engines.
JKII uses Quake 3 engine, HL uses a highly modified Quake 1 engine. I don't know if the models and skins will work or not, but the game play would not change with new models, it would just look real cool.
And TFC is a good game, CS is a good game too. You may prefer CS but that does not mean TFC is "abysmal" you just don't like it, it is a harder game to play then CS which is probably why you don't like it.