As in the comics, I feel that you ultimately do your main characters a disservice by adding 'clone' characters, particularly when they are as or more powerful than the original. IN the short term, you get some nice stories. But in the long term, the uniqueness of your main character is undermined.
Obviously, given that Supergirl is herself a clone character, the above thesis is a bit problematic in the case of Supergirl. Nevertheless, there is no need to keep adding clones like Martians, Daxamites, and other Kryptonians.
This show would ultimately better if Superman and Kara were the only Kryptonians who ever appeared. You can add Martians, but go the JLU route from the DCAU and downplay their Superman-type powers and focus on their shapeshifting and TP. There was no need for Daxamites.
Superman should be clearly more powerful than Kara, probably in every respect, though it might be OK to give her a few areas of superiority (if explained properly). But teasing that Kara might be more powerful is a cheap way to generate interest in her. She's supposed to be in his shadow and trying to find a place for herself despite him being 'the man'. Superman's immense power and his nearly ideal character are what make his shadow so long and hard to escape. That's where the tension is in her character arc--making it so that she is ultimately the most powerful changes the nature of the key dramatic tension that defines the Supergirl character. This is about her finding a way to shine despite being number two--not about her becoming number one, or even number 1(B). That's too easy an out. Fortunately, while the show seemed to be taking the Supergirl > Superman route early on, they later backed off of that. Even with Martians they seem to have slowly returned to Kryptonians > Martians, despite suggesting the opposite earlier on. But this remains in doubt, and at any rate, Martians are still too close to being on the same physical level as Kryptonians, even if ultimately less powerful.
The Flash has it's issues here as well, with too many speedsters. At least in Arrow, Ollie is clearly the bow guy and much better than his sister. And Speedy never became another Green Arrow.