You and mom should both be there for bedtime routines for awhile. She will either be fine with it or not. Either way, have the both of you do the whole routine for awhile and then I would try having some nights where you both put her down, some where just you do (but have mom pop in at the end for the good night kiss) and some where just mom does (but you pop in for the final good night kiss.) The most important thing is to teach her to be flexible with who is there for the bedtime routine (though the routine itself should be consistent, so make sure you compare notes on what happens during the routine!)
Bottom line, this is not unlike any other sleep issue that parents face with young children. She will need to learn that it's okay to let dad put her to bed, and she may not like it (kids don't like something out of their normal!) but will need to learn to be okay with it. It will probably be some nights of fighting and crying before falling asleep so you guys will need to be okay with that or mom will be stuck dealing with both kids sleep issues solo for ever :)
Also - it reallllly sounds to me like the real issue is not who puts her to bed, but about her not having good sleep habits. You and your wife really need to work on establishing good sleep patterns (appropriate bed and nap times, teaching her to fall asleep on her own, teaching her to stay asleep, to sleep in her own bed, etc. etc.) unless you want things to continue as they are (and be amplified when there's another little being needing your help to sleep!)
Being a parents does NOT mean you need to always be tired and underslept - you need to teach some good sleeping skills and it will not be easy because she has gone two years without being expected to develop any of these skills. Please get and read the book "Healthy Sleep Habits, Happy Child" by Marc Weissbluth. Read, read, read, before the baby comes and make a good plan for fixing these issues. For your sake as well as the kids'!!!