I think it has a lot to do with your age though. Despite what people say, it's hard to get a proper profound relationship around that age because everything else is working against it and pushing you to just be casual and "enjoy life".
That fact is, relationships like that are rarer than people claim. It's hard to meet someone with whom you connect totally.
I still think about ex-girlfriends I was with 7 or 8 years ago. It's a part of life. You can't just brush aside a past relationship as soon as you start the next.
I'm also wondering if you still see this ex of yours. That's not going to help things. This is just me guessing but I'd say you're just not in the right relationship: after what you had with your ex, you might have chosen a simple and comfortable relationship, grew close to this bf but there was never that spark that there was with your ex. I really think this should make you question your relationship: you've given it 3 years. Sure, some people find it hard to start a new relationship right after a breakup but this is a whole different matter: 3 years is really long.
People don't get over their exes completely but I can assure you that if you're patient, look out for the right person, you'll meet someone who, although he might not erase your ex from your mind, will make you realise that what you had with your ex wasn't as special as you thought... and that you could something just as special if not more special, with someone else.