I dont really care for Supergirl other than the fact that she is hot. Power Girl is even hotter. As Clark's sidekick and the only one who can really get him (being alien and all) i think she is fine, better than Superboy anyway. I like how Clark sees her as his only link to Krypton and his real family, and how he is overprotective of her. Besides, Supergirl usually hangs out with the Outsiders (isnt that the team she is in?) and barely fights alongside Superman, so its really only Kara and not Supergirl that appears in his stories.
This reminds me of the Robin debate and whether he is important to the Batman mythos. Well Supergirl isnt as important as Robin, but it wouldnt hurt if they introduced her at some point, maybe in the 3rd film. Besides, she doesnt have to be Supergirl, since its not about her fighting with Superman, as it is about Superman getting a cousin, how she adjusts to Earth, etc.
As for Clark being the last Kryptonian, well it was a nice concept at the start but they ended up giving him a lost cousin, a dog, and a bunch of villains from Krypton so the idea that Superman is the sole survivor is one that he has until the others appear. And i say, get over it because everything that this notion implies will be examined in Clark's origin and first years. Even in the comics he is still raised alone, he still feels like an alien on a foreign planet, etc. When Kara appears all the character development revolving around him being the last K is already been done. But even with Kara, he still feels alone, he still wishes he could be on Krypton and he is still overprotective of his adoptive home world, Earth.
So what i mean is that since Kara appears later on, she doesnt change the fact that Clark has been the sole Kryptonian on Earth for at least the first 30 years of his life. Kara might break that absolute but she is not enough to change things too much. She is still one person, not a whole team of Kryptonians (all the others are villains anyway).
And then, introducing other Kryptonians give us a chance to further explore life on Krypton and important parts and characters of its history, like Jor-El.
Oh btw, Supergirl or no Supergirl, Clark's gotta have Krypto the Superdog. Krypto is just awesome.