If you are working on an alternate transcipt, which it sounds like you are, make sure to get A's in those classes.
Also, a cum 3.0 isn't awful, and it depends on your major. As you've said, you have a 3.4-5 in your major GPA which will be very good. You can also choose to use the optional essay to address your low GPA in some classes. I would recommend not using that essay as an excuse, but rather as an opportunity to sell yourself and show how those classes and poor grades tought you what it takes to succeed in the academic world and business world.
With a 3.0, it will be important to score well on the GMAT, but ultimately GPA and GMAT are only 2 criteria in an application process that has many criteria. Everyone usually has a weak criteria or 2 or 3, so make sure that you work your hardest to be the best YOU can be in all the other criteria (aka essays, rec letters, GMAT, extra curriculars, leadership, work experience, etc...)
Also, check out our thread on low GPA success stories: low-undergrad-gpa-success-stories-79977.html
We've had many low GPA applicants get into top 5, 10, and 20 schools. You could be the next
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