What features should be included in your actual accomplishments and skills to be accepted in a top university like MIT I was wondering about
 how can one apply for a PhD program in a top ranked university.
I can tell you about a namely accomplishments and skills which is labelled as 'very good' for a graduated M.Sc student in an average university so that you can consult me and the people who almost have a similar accomplishments and skills.  

To be more precise I would like to know:  


How can one be accepted and get the scholarship for a very top-ranked university like Berkeley, MIT. For example are the following accomplishments and skills satisfactory?  
If not, which points should be added or improved generally?  
How much is it matter how old are you for applying for PhD at these places?  
What features differentiate the CV of someone admitted to a top school (MIT)versus someone admitted to an average school (Calgary Canada).





Two ISI papers Including one 'Power systems, IEEE Transactions
on ' and 'Electric Power Components and Systems'.
IELTS and GRE meet the minimum requirements. 
Having a very strong recommendation letter. Also, my supervisor professor is one of the top (top 50) in his field.
Two years teaching experience in a small university as a lecturer.  


P.S. I have B.Sc and M.Sc in Electrical Engineering.
Although your question doesn't specify it, I assume you're looking for admission to a top-ranked PhD program in electrical engineering.  I'm one step away, in a top-ranked program in computer science, so take my answer with a grain of salt.


  Two ISI papers Including one 'Power systems, IEEE Transactions on' and 'Electric Power Components and Systems'.


Since you already have a master's degree, having a couple of publications is a minimum requirement for admission to a top PhD program.  Where the papers were published is of secondary importance (although your emphasis of "ISI" over "IEEE" is a little worrying).  What really matters are the actual results in the papers.  Are they good results?  Are they well-known to people in your field?  Are your papers likely to be highly cited?


  IELTS and GRE meet the minimum requirements.


"Meet the minimum requirements" is not what top programs are looking for, on any axis.  Fortunately, test scores don't really matter all that much (except, at public universities like mine, the spoken English test).


  Having a very good recommendation letter as my supervisor professor is one of the top guy (top 50) in his field.


The fact that a top guy in your field wrote the letter matters far less than what the letter actually says about you.  A weak letter will kill your chances, especially if it's written by someone well known in your field.


  Two years teaching experience in a small university as a lecturer.


Hmm.  Okay.  can't hurt.


  If not, which points should be added or improved generally?


You really haven't given enough detail to point out anything that needs to be improved.  What matters most is the quality of your actual research contributions, and that's just not deducible from the information you've given.


  3) How much is it matter how old are you for applying for phd at these places?


Not at all.  Age discrimination is illegal in the US.


  4) What does a namely CV should contain when applying to a top university as opposed to one that is an average university (like Calgary Canada).


I assume you mean "What features differentiate the CV of someone admitted to a top school versus someone admitted to an average school?"  (No matter where you apply, your CV should accurately and honestly reflect your accomplishments.  Don't add bloat.  We can tell.)

You may be able to gain admission to a lower-ranked school on the basis of grades and test scores.  But the competition for admission to the very top ranked schools is absolutely fierce.  (My department gets 2000 graduate applicants per year, from which we admit about 100 PhD students and about 50 MS students.)  If you want to be admitted, you really have to manifest like a successful PhD student already.  You don't just want papers.  You need  high-quality, high-visibility, well-written results, ideally which would not have been possible without your contributions.  You need the beginnings of a well-reasoned and compelling research vision.  You need to display intellectual strength, depth, maturity, and taste.  Well-known leaders in your field must sing your praises in technical, personal, and credible detail.

If you have all that, your CV will take care of itself.