Short answer...D used to be called A, E used to be called B.
Longer answer...The three concourse of MKE have been there as far back as I'm aware -- perhaps back to the 1955 terminal construction -- but they were hallways with small ground-level holding areas at the end for planes to park around.
A (today's D) was the first concourse to be built to modern standards with eight second-story gates A1-A8 and seven jetways, probably in the early 1960's. It ran as far as today's D38. Milwaukee's two big-hitters, Northwest and United, used this. All gates were upper-level and what is today the lower-level walkway and D27/28/29 was offices and not public-accessible.
B (today's E) was the second to be modernized. It was North Central's (later Republic) and again it was essentially a hall with ground-level boarding. The rotunda was added in about 1970 with six jetways for a total of 8 gates, B11, B12, B14-19.
C (today's C) was, like the others, just a stub with ground-level boarding. It was modernized last, with 8 upper-level jetway gates built around 1975, C20-C27.
At that point Milwaukee's concourses were (left to right) C, A and B which was a little confusing being out of order. But what really pushed the airport's hand was Northwest's request for more gates on B (today's E). The rotunda only had 6 gates at the time, and the diameter of the circle was expanded outward to fit in the 8 gates we have today. But B already went up to B19, and adding two more gates would have been B20 and B21. There already was C20 and C21, so something had to be done.
So -- the new lettering and numbering was devised. C remained as-is with C20-27, A was renamed D with gates D40-48, and B was renamed E with gates E60-69. If new concourse were ever to be added to the north/west the letters A and B were open. And new concourses to the south/west could be F and G. Keeping the number ranges so far apart made room for expansion, which was a move with the longer view in mind as well.
D got the hammerhead in about 1990, and gates were renumbered 30-56. Then years later when the lower-level gates were added in the stem (replacing upper-level jetways on the south side of the stem) they backed into D27/28/29.
C got their hammerhead in the mid 2000's and gates on C were renumbered from C09 through C25
So while it may seem odd that there's no A or B, what's left are three concourses which are lettered and numbered sequentially. All the growth was accommodated within the system. It's not likely MKE will need more gates in the foreseeable future, but if they ever do the letters are available to keep things in synch.