I think the debate is inevitable. Not that there's anything wrong with it. But Methodists and Baptist are, in many ways, very different. Wesleyanism and Calvinism, Anglicinism and Puritanism, are polar opposites. And though there are variations; Methodists draw from an Anglican-Wesley Emphasis and Baptists from a Calvinist-Puritan Emphasis (even if many Baptists aren't expressly calvinist) so it's only natural that as those two traditions grew they would remain very much different. If you had asked, for example, the difference between Anglicans and Methodists or even Methodists and Roman Catholics I think you would've found less 'debate'. Though we differ from those two traditions (Roman Catholics more than Anglicans); we share common roots and many common traits, look at the Bible in similar ways and, in my experience; get along pretty well. (In my particular setting Roman Catholics and Methodists get along great; since we consider the RCC our cousins; and the Baptists in my area view the RCC as the spawn of Satan and the enemy; even preaching against them, one church having a sermon series on 'cults' and including Roman Catholicism in there.)
At the end of the day though; in my experience, both sides are willing to work together for God. Even though we vehemently disagree with the very fundamentalist Baptists in my community; we work side-by-side with a local homeless shelter funded by both churches and we're willing to recognize that Jesus' call to care for the poor is a universal call across denominational lines. (Although, admittedly, many in the Baptist church, though currently not it's Pastor thankfully, feel they should not be supporting the homeless shelter because it 'enables lazy people' But, if I dug deep enough, I could probably find someone who felt that way in my church, too).
One thing though I've found, is sometimes the laity have no idea what the differences are or even what their personal theologies are. I used to have a parishioner who I earnestly have no idea what they were doing in a Methodist church. Anti-women (to the point he felt women should not vote, and not in a sexist-joking way, in a very serious, adamant way. He genuinely thought it was an atrocity, they weren't capable of voting), a bible literalist/inerrantist. Vocally rejected connectionalism and frequently told me and others he thought the church ought to govern itself and that the Bishops and the DS were "unbiblical", and so on and so forth. But he was a lifelong Methodist. Chances are, he was only there because he was raised there, and figured ones denominational affiliation was like ones blood type. You're born with it and you can't change it. Discussions like this one make me wonder what people who didn't know about Methodism, who knew him, thought about Methodism. They might think Methodists are just like the SBC!