I cant comment on the midi portion of your question since when I have used the 5000 it was connected to a midi patch bay with 7 other devices and not acting as a master.
BUt I can say that it does EVERYTHING else SLOWER than my 2500.
my buddy and I go back and forth on this.. he absolutely LOVES his 5000, yet gets mad jealous when I show him JJOS features. then again, he is one of those kinda naive "have the top of the line" kinda dudes so.. I suppose some of it for him is the ignorance of being able to boast a bunch of "flagship" features........ that work poorly or are insignificant at best.
The funny thing is, when I bring up something like the added features of JJ, he'll reply like "ahh well I can do that in my Daw better, blah blah, but then thinks that the Mediocre synth in the 5k is worth bragging about as if I cant do that on a real Synth better. hahahahaha
actually I just realized I need to slap him.

but yo for real.. everything I have done on the 5000 feels slower and not as fluent to use as compared to my 2500.
Looking at the large screen is great, but even the layout of some of the buttons are annoying, like the open window key and the mode button being in different places.(and to me less easy to access quickly without thought).
But mostly it boils down to work flow.. and to me its mad contrived on the 5000. so if I had to trade my 2500 for a 5000 I would not. at the same time, the bigger screen is very nice visually, but the extra Q-links are meaningless to me personally... extra vol/pan params via mixer & track mixing.. blah blah.. the synth blah blah.. 8 audio tracks in a slow environment with a buggy OS.. blah blah... I mean its mad nice to say I have the "best one they make". But in 2009 when referring to NuKai's Flagsh!t model mpc5000.. it just doesn't mean what it used too..
Basically a 2500 with JJ will pretty much do everything the 5000 can do and better with less issue and WAY increased workflow.. minus an insignificant HW feature here and there.