I don't think you're punishing the kids with the alternating weekend idea. They need their mother too and you're giving them what they need. What she chooses to do with the time she's given with them... is beyond your control. She'll reap the benefits of her interactions (or lack of) with the boys later on in life. What's best for the kids is the presence of both parents in their life.
Also, I agree with you, you're going to need that for your new relationships in the future. What's best for the kids is that Dad is happy and enjoying life. If Dad is alone and sad, how's he going to be able to demonstrate a healthy, well-balanced life to his sons?
Nah, IMHO, keep pushing on the custody you want. She's controlled you and had everything her way to this point. Fight for what you want and know is best for the kids. Never give up.
M:11 | T:12 | Status: Married 4C's of WAS communication: Cool, Calm, Collected and CONFIDENT