[moomber123]

A few things:
1.) Case Western's professors have a strong European ties. Professor Lyytinen is from Finland, and Professor Bolland is a fluent French speaker. They both publish substantially in European journals, in particular, EJIS. The ranking methodology here typically has an "American bias," which tends to put EJIS on a second tier. Most ranking only uses MISQ, ISR, and perhaps JMIS as the only A journal outlets for IS research, which can substantially underestimate the output for department like Case.
2.) Case Western IS is a very small department. There are only 3 professors. For those ranking that has some "reputation" factor, this is not a strength. But it is not hard to find ranking, especially for PhD level ranking, that eliminate this rather useless measure.
3.) Case Western IS is now heavily focused on new "revolutionary" type of research, tying IS research to design. They actually have hosted a few conferences, workshops for a few years already, in which IS researchers and designers, architects, got together. This is a very "unorthodox" way of doing IS research, and in all likelihood is not yet considered to be an impressive achievement by the "mainstream" or "establishment" in IS community. However, if you look closely at the participants, you'd find participations by prominent management/business scholars, like Karl Weick from Michigan. I guess this is an example of "exploration" vs. "exploitation." Whereas other established IS powerhouses "exploit" their existing strength to continue their dominance, Case is doing "exploration" works that are still in the process of gaining legitimacy. True, it is not necessarily a safe choice, as far as career development is concerned, because you never know if this type of research with heavy emphasis on design is going to gain traction, but I believe academics should be more about idealistic pursuit of excellence than just mechanically twisting things around to add items on CV. You will never find "idealism," "sincerity," or "extent of scholarly conducts" in those rankings, or else Case Western would come out much highly rated.
4.) Any ranking that takes placement into consideration would greatly harm Case's ranking. MIS in general is still struggling to recover from the hiring hell that started since the dot com bust. Placement for MIS doctoral students is still exceedingly difficult. In times like this, top schools are unlikely to hire from schools with no "pedigree" anyways, but teaching-oriented schools would prefer big school names over academic productivity. The result is that top schools hire among themselves, and middle-ranking schools take what the top schools did not pick up, leaving schools like Case in a very difficult placement situation.
5.) MIS is a highly fragmented field. There are people doing almost engineering-like research at Arizona, and at the same time, there are people doing almost OB like research at Minnesota. Most likely, they don't even know what the other group is talking about. They don't publish in the same journals, don't hire from each other. Case is more behavioral-oriented, but it's not exactly an OB shop. So in that sense, it kind of finds itself in a tough spot looking for a niche. This is not uncommon among some upper-middle ranked schools.
6.) I suspect the poor economic state in Cleveland, or in Ohio in general, has something to do with the declining prestige of Case Western as a university. A lot more prominent scholars come out of Case in distant history than in recent time.

In general, I find the rankings for PhD programs to be of limited use. (well, for all kinds of programs, this statement could be true to some extent) Ranking is inappropriate when you think program ranked number 21 is necessarily worse than number 20. I'd suggest taking ranking from a rough "tier" and treat schools in the same tier equally, and then focus on the research focus, the style, and the people in the departments. Case happens to be a hidden jewel, especially that many Asian students who are very competitive in admissions tend to take ranking far more seriously than they should, and pass on Case accordingly. This ends up limiting Case's reputation to those who interact with them directly.