So here's my situation: I'm a senior electrical-engineering major student in a decent-ranked university (60-80), and I've been working in a lab in our department and published 2 papers as the second author (conference paper, IEEE) and currently I'm in charge of two projects so I may publish more before I graduate. The thing is: I have a low GPA (2.9), but there is a reason: I've been an athlete of the fencing team in our university, and for two years I've been the vice captain of it. I have to go to practice every night, Monday to Thursday, so I don't have a lot of time to study. My boss, who got her PHD degree from CalTech, trusts me a lot so I will have a kickass recommendation. She refers me as a student who's "not very good at theoretical learning, but always creative and can solve practical problems very well." She also granted me the fellowship. I want to go to those well-ranked engineering schools, like UIUC or Berkeley, and pursue a master's degree (and even a PHD, if possible). Although I do have a good research background, I'm worrying about my gpa. Most schools do have a gpa threshold, but is it possible for me to get into these schools? Thank you.
You can file for academic petition where university will initially reject your application but an academic committee will review it and may give you conditional admit. What happens in these cases is if you get more than 3.0 GPA in first sem , you are in the program permanently otherwise you are out.It may be better to speak with the department or program coordinator to get better understanding of this and they may have prior knowledge about these cases and may let you know if there is a good chance of your getting petition getting passed or not.
Alternately you can go to industry and work for couple of years before applying. An Industry experience definitely will add more value to your application and will show the committee that you are a serious candidate.