What is, currently, the best choice to run MIDP applets in a Windows CE based System?
I believe the ONLY choice available to you is SuperWaba/TotalCross.
WebSphere Micro Edition might also be available to you if you're an IBM ISV Partner.
We use IBM's J9 JVM on Win CE. You don't have to be an IBM ISV Partner to get it. You can buy it from IBM partners like the one we use. Here is a link to Microdoc's site showing the platforms where the J9 JVM is available. http://www.microdoc.com/products/certified-me-runtimes. We've been very happy with J9.
In my experience IBM's J9 is the best - I've used it to support MIDP/CDC apps, but the profile/configuration combinations supported include MIDP and Personal Profile, and both CLDC and CDC Foundation.
In contrast to other opinions, there is not a single choice of VM if you Google around. But I went for J9 because it proports to follow proper Java compatibility, unlike SuperWaba that is basically a Java variant so your 'Java' apps would be less portable.