Fixing Bad Sleep Associations is Difficult but not Impossible
Bad news first: Fixing your son's sleep problem is not going to be easy. I'll give you a little boot camp tough love here and tell you, "Welcome to parenthood, where nothing that you thought would be easy ever is." That said, it's not impossible and this is just the first of many tough situations you'll encounter with your child. When it's over and you have a great sleeper and everyone in the family is well-rested and happy, you will look back at how hard it was and know it was worth it.
First, you should sit down with your wife and get on the same page with her about what you both want and how you both really feel about the sleep situation. Sit down with pen and paper and count the hours of sleep that everyone is getting and if you miss her presence in your bed, then let it be known and don't feel bad about it. At 28 months, your son is capable, with your teaching, of falling asleep on his own and you have every right to want your wife in bed with you. Your wife also has a responsibility to herself and her family to take care of herself and that includes getting adequate rest. So many moms complain about feeling sleep deprived, but we don't realize that sometimes we're a big part of the problem.
Next, both of you need to alter your perception of who is in charge of this situation. Parents of toddlers often get stuck in this trap. It seems impossible to control toddlers or to get them to do what we want sometimes. I have heard it in the language of many parents and I can hear it in yours, too, ("we had to sleep with him in his bed otherwise he would not stay in his room" and "but lately he will not go for it and it results in tears"). We fail our kids, however, if we allow them to do what they want just because they're louder, they cry or they outlast us. We are the adults and we must set rules and limits for their own health, safety and mental well-being. We also fail them if we are too strict or callous and allow them no room to make mistakes and learn. Balanced discipline is key in these situations, but in the end, you're the one in charge of discipline, not your toddler.
Finally, make a plan and implement it consistently. If you and your wife decide that your son needs to fall asleep in his bed without mom, then you've got a goal in place to work toward. Get ready for some hard but rewarding work. I'm going to suggest a few ways of getting started: