Answering this question and reading an answer by Ero Senin made me think some more about chakra natures. Will attacks that use the chakra type that the user has a natural affinity for always be stronger than attacks that use other types of chakra, even after mastering these other types?
Answered for if the first chakra nature will be the strongest attack of a ninja?
There is no such thing as FIRST Chakra Nature. Each and every individual has a chakra nature that he has an affinity for, and he can master stronger Jutsu of that nature with much more ease as compared to others.
To prove my point, what was Sasuke's first chakra nature modification? It was Fire. but he learnt it after a lot of effort and Uchiha's have the inclination towards Fire Jutsu. But individually his chakra had an affinity for Lightning nature and thus he has a larger variety of Lightning chakra moves and mastery.
Thus a ninja will have a single nature towards which his chakra leans which will be easier to master. Strength is more of an effort effect. For similar strength, he'd have to work harder to master any other chakra natures...
An exception I can think of would be Bloodline Chakras. I don't think there is any difference in strength of different natures inherited as part of bloodline. Yamato using Wood, should have similar competency with both Ground and Water chakras.
EDIT: I remember Kakashi saying something to this effect during his battle with kakuzo. What he said was that Kakuzo has used such strong Lightinng and fire attacks which can't be used unless the user has natural affinity to that chakra nature. This means that the strongest attacks of each chakra nature will not be mastered unless you have a natural affinity for that nature.
What I am trying to say is that the jutsu of same level will have equal power(strength), but the natural affinity. But higher level jutsu can only be mastered if and only if you have natural affinity for the chakra nature. Thus absolute mastery of other chakra natures is not possible.