Why are your only two options 'let's get back together', and 'no, never, it's over'?
You raise a valid point: You met when you were babies, got married when you were babies, and of course now, you're not sure who you are without him as an adult on your own. Of course you feel conflicted.
This is what you should do: Have a conversation with him. Ask him a few pointed questions: How do you know that he won't [do whatever it was that made you separate] again? What has changed? How has he grown? In what ways will he do better? What would he do differently if you decided to give your marriage a second chance? Can he be patient with you while you sort out your mind (I did NOT say your heart. Right now, 'follow your heart' is a bad idea. You really really need to use your head.)? And ask these questions of yourself. Seeing as how you admittedly neglected the marriage, what are YOU prepared to do? In what ways have you changed? What would YOU do better or differently if you decided to give yourself, and your marriage, a second chance?
It sounds like you two do have a kernel of affection still, and if you have that ... you stand a chance. As much as I empathize with you feeling responsible for both of you, you're not. You are only responsible for YOUR choices. Granted, they affect him, but HE made choices that led you to separate, too ... right? You both have to recognize how you contributed to where your marriage failed, and decide if a) you're both ready to re-commit to doing things differently, and b) if you're both reallyreally in this forever? Ask him if he can imagine his life without you in it. Ask yourself the same question.
I think I can articulate your exact dilemma: You want your marriage, but you want a different one. You cannot go back, and the idea of reconciling ... but ending up right where you were when you separated is what makes you want to walk. When you have this conversation with him, start there. That you miss your marriage. You miss what was GOOD and fun and positive and sexy ... you miss the good stuff, but you cannot and will not get back together only to backslide in a year or in 5 years. You BOTH must do some work on yourselves, and determine your biggest mistakes so you can move forward not repeating them.
*big hug* Just talk ... and see what he says. I do, however, strongly suggest staying clothed and in public places for a while. Even if you do decide to get together again, just DATE each other for a few weeks. Pretend you're just meeting, because in a big way ... you are.
Best of luck to you.