So for clarification purposes, you want traditional Masters programs? Not SMPs correct? Since you have such a strong sGPA, boosting the GPA even graduate GPA isn't what you're looking for but to simply obtain a Masters in something? Or am I completely off base here?
Your adviser is probably as good as most: not very good. If your cumulative overall and science GPAs are strong, then more academics doesn't change your app. If your MCAT isn't competitive, then retaking the MCAT can save you at least $25k vs. a grad program. Did you apply early (June)? Did you apply broadly (10-50 schools)?