Hello Wellbehaved~
I agree with BB, it's time to sit and have an honest conversation about your relationship and whether what you share compensates for what is lacking. I too find it odd your boyfriend said "how kind and smart and attractive my new friend is, and how he'd rather see me romantically involved with him than anyone else."
It sounds like your boyfriend knows you are not fully happy in your relationship, and knows either a) he can't give you what you're wanting because it isn't his personality or b) he won't give you what you want because he doesn't want to.
I'm gonna say it sounds like a. He knows it isn't his personality. You said you liked him in the beginning for his empathy, which he still has, not because of an intellectual conversation.
My suggestion to you is this: figure out what you want to do, do you want to pursue this relationship any further with your boyfriend? You're not married so it's a lot easier to leave now, rather than after that happens and you have to be granted permission from a judge to break the ties. If you choose to stay with him, I'm sorry but you will have to let the new "friend" go. You've already stated you both (friend and yourself) know you're attracted to each other and interested. It's nearly impossible to remain "just friends" while trying to work through your relationship with your boyfriend.
As for the boyfriend and his online sex...men are physical women are emotional. Yes, both share those traits but not to the same extent most of the time. If you're not keeping his attention in the physical aspect he will look elsewhere for someone else to fill that spot, just as you did for intellectual/emotional. I was in the same boat as you with finding someone more intellectual so this advice comes from the heart even though it's hard to hear.
If his conversation with his ex was purely empathetic in its basis and not romantic saying such things as "I miss you" or "I love you", again, his ability to empathize was your first attraction, can't fault him on that.
The love goggles come off after about a year and we start to see our partners with flaws our brain was able to blind us with when we are in the first stages of love. It sounds like that is what is happening to you now. You're starting to see him for what he is rather than what you think/hope he is. This new man has flaws too, we all do. You're unable to see them at the moment because of your infatuation with his intelligence which creates an emotional connection for you.
Being life partners whether someone is married or not isn't about great happy times and lovey dovey moments. Ask yourself this with your boyfriend...Does he respect me and do I respect him? Do we put each other down? Do we support each other's dreams, goals, and aspirations? Do we want the same thing when it comes to retirement? Where do we stand on politics, religion, children, family values, or the role of partners in marriage?
So many times we feel like we have to be in love 100% of the time to have a happy lifelong marriage. Honestly love and being in love is little pieces of lifelong partnership. The intellectual/emotional connection you're missing with him you can find in your relationships with friends. I'm only 32 and just now starting to think about all this, it seriously helps talking with older men and women about relationships. They have lived, loved, and lost. Perhaps find an older woman to help you work through it and see what is really important in life.
I wish you all the best as you find your way through life's challenges.