What an interesting question...
For me, I love the good times I had with my ex. We really got along well and he was a wonderful companion when things were going smoothly between us. Those are the times I miss the most.
The bad...it reminds me of just how bad things got between us, so I can remember that there was much not addressed or completely swept under the rug in regards to having a marriage. And for me, it was too much, which is what made it "bad" in my perspective. Bad enough to outweigh the good, at least at that moment.
How to reconcile both - well - its just life. Good things have a down side to them too. I really like my job, but I have some issues with it that I know I can continue to ignore or step up and address. Same with my relationships. Nothing is perfect; we are all flawed in our own ways.
Over time, things balance out way more than they do when we are in the thick of it all. Memories fade and have less emotions tied to them. I think time is the ultimate reconciler.