For me, one of the biggest benefits of importing a gedcom has come from maintaining the connections between generations (and with siblings) that had worked out when I added the people in genealogy software. (When a family uses the same first names over and over, it's way too easy to get individuals mixed up, so once I've gotten them properly sorted in one place, I want them to stay sorted when I add them to WikiTree.)
If your existing data is in an Excel spreadsheet and you are importing alphabetical groups, rather than groups based on branches on your family tree, it seems to me that you miss out on that benefit of a Gedcom. And I can imagine that the parsing functions in the tool you use to convert from .xls to .ged format and in the WikiTree Gedcom import system might not be effectively interpreting your data. If I were you, I'd try sharing a sample of your spreadsheet data (in both .xls and .ged format) with the WikiTree team so they can test it with their new protocols for working with Gedcoms.