If you step over a MapEngine call, it won't return to the debugger because MapEngine() runs its own loop. If you use the analogue.js included with 1.7 you can set breakpoints inside map scripts though.
we now have a 99% compatible replacement for the vanilla engine
It's tempting to want to wait until Sphere 2.0 has stabilized to commit to anything, but part of the reason I took the initiative with minisphere in the first place was because that process was going nowhere--note the sorry state Pegasus ended up in.