I think it is great that both of you are open to a more unified Church. I would also like to see a greater unity in the body of Christ.
The snags are going to in the recognition of ministry (ordination, pastoral leadership etc.), our differing understandings of the sacraments/ordinances, and our polity differences.
I know that many Baptists view polity as being simply human made conventions for organizing the church. But a lot of other Christians see their polity as having Biblical roots. Those of us with an episcopal structure wouldn't abandon that for a congregational structure (or visa versa I'm sure.)
Also while many Baptists don't have a system of ordination or recognition of ordination (at least one exception being the ABC/USA which does have a system of ordination recognition) many other denominations do. So what does ordination mean, how someone is ordained, how that is recognized, and what authority that gives the ordained would be big questions to deal with.
The Baptism, Eucharist and Ministry document by the World Council of Church from 1982 tries to address some of these issues.
http://www.oikoumene.org/en/resources/d ... -lima-textWhen my denomination seeks a "full communion agreement" with another denomination a big part of that is coming to a common understanding about ministry and about the sacraments. In the UMC, ELCA, PCUSA, the RCC and the TEC your ordination has to be accepted by the denomination for you to be able preach, baptize or preside at Holy Communion in their church.
I know Sandy you probably view this as simply human traditions but most of the denominations I've listed don't see it that way.
In any kind of merged denomination how someone becomes a pastor of a local church (congregational election, Presbytery and Session election, appointment by a Bishop etc.) are also huge issues.
I'm not saying we shouldn't seek unity. But everyone isn't going to abandon their historic theology or polity to do that and many non-congregationalist don't believe congregationalism is actually a Biblical model for the Church any more than Baptists think that the episcopacy is a Biblical model.