One reason to keep Domino is the security is significantly better than any technologies I have ever known or heard of. Combined with the Lotus Notes client it is just about impossible to break.
Most of the technology being dreamed up now to address web growing pains have been in Lotus Notes since 1993.
Biggest negatives are that the programming of the system is so easy bad developers can get away with putting systems into production that should have never been put in production. Second biggest negative is that since it is a workflow enabled document based paradigm most programmers don't understand it. Third biggest negative is since it has such broad functionality it takes better quality of administrator and developer to do a good job with it.
To completely replace Lotus Notes/Domino with say Microsoft products would take Windows Servers, MS Sharepoint, IIS, SQL Server, Exchange, Outlook and Internet Explorer and all of this would need to be redundant since Lotus Notes / Domino is already fault tolerant. Not to mention an army of administrators and developers to program and maintain the systems. Therefore you would have a large constituency to defend the new bureaucracy.
So when you look at it in that light, maybe there is much more "wrong" with all the technologies it takes to replace it than the three biggest negatives I know of with Lotus Notes/ Domino.
FYI: Lotus Notes / Domino data storage and programs have been forward compatible since 1989. In other words, an application or database in production in 1989 will still work with today's technology so you aren't always having to rewrite and convert so my guess is the ROI over a long time is extremely high.