He is a great guy means what exactly? No don't tell me I personally don't want to know. This is something you should ask yourself. I strongly suggest a pen/pencil and a piece of paper to write down those qualities you see that make him a great guy and make him the potential 'The One'. Once you have that list, then ask yourself:
'Is being a bottom for life something I would want with all of these qualities that also come with the package?'
Sex is far much more than 'getting off'. Like it or not (most gays flat refuse to even consider it) our roll in bed has much to do with our sense of security or to be the security giver, our need to be 'taken care of' or 'care for' the other. When a guy wants to be inside of another guy there is a lot more going on there than just sex. When a guy wants a guy inside of him, again there is a lot more than just sex.
There are needs and wants beyond mere animal lust and the momentary pleasure of the climax. It is a very complex thing, emotional, spiritual, physical, all of this on many different levels.
So I ask another question: What do you get out of sex?
Again, don't tell me, I do not need to know. You need to once again make a list, make a searching and fearless list - an inventory as much as you can, include how it feels when X takes place. Not just the pleasure bit, but the deeper emotions.
Then ask yourself if you can actually live without/with these emotions being satisfied then weight those against the earlier list of his being a 'great guy'.
Can it work, yes, if you can see the potential relationship being rewarding to you emotionally and spiritually in other ways. Will it be easy? Unknown, not until you figure out what it is you get out of being Top/Bottom and figure out if you can pass on being the top.
Also don't forget to communicate with him your concerns. He might be willing to bend a little, a little give and take should happen in a healthy relationship. If he cares about you, he might be willing to do for you that he won't with others.