Well, the D3 in SFC3 is "similar", the changes are pretty much, removing the Pirate layer from OP, adding the ability to supply at allied bases, not just your own, and then the big one, the only place you can get a mission is in a hex with an enemy AI. This causes you to not be able to take hexes in an orderly manner and ends up in a checkerboard of hexes as you try and move into enemy territory. I also seem to recall that because they gave a "pilot" to planets it caused issues with being able to take them or something. There were problems with how it was done, imo.
Other than that there is also the ability to outfit your ship with your choice of weapons, but restricted by mass, but only in a very general way, which doesn't make sense in any way, to my mind. There are other additions like the readdition of officers to SFC, as well as being able to see general chat and race chat at the same time. Then, there is the tactical portion... we won't go into that.
Not worth the massive amount of money you have to pour out for it on ebay to get it (because it was discontinued and is in low supply). You're talking like 80 bucks or more, ouch.
There could have been some other changes, but the fixes and additions to the Dynaverse just don't compensate for the rest of the games lack of extended playability. Just my opinion (and that of everyone I know, personally).