(Second hand, from my conversations with him a dozen years back)
Issues with rampant anti-calvinistic bent, separation from worldliness, sectarianism (he didn't go to an SBC undergrad so wasn't part of the clique of SBC), denominational hierarchy, liberal tendency away from inspiration, lack of strong doctrinal teaching.
We were many years at FBC Dallas (SBC under Dr Criswell) as my kids were young teens. They saw the weakness in separation and lack of deep doctrinal teaching in the SBC in general, but we were blessed at FBC to have Criswell College and uber-conservative folk. Kids noticed at SBC camp for our county that everything was "simplistic" and no depth.
And I personally fellowship with the Founder's Group of the SBC and attended many conferences. My church today is closer to SBC than anything (no affiliation) but only with the Founder's type. Many local SBC pastors are like those my son saw in the class in seminary.