I'm not sure what can of worms I've opened here...
Anyway, in terms of single player gameplay there appears to be no difference between SEF2000 and EF2000 V2.0.
In MP though, on the surface the big difference is support for TEN (Total Entertainment Network). Whether this makes SEF2000 incompatible with EF2000 V2.0 in multiplay, I don't know.
They do appear to be incompatible. I tested on my LAN with EF2000 V2 as host and SEF2000 as client. The client saw the game, and seemed to be able to join, but I never saw the Join from the Host screen, nor did the game launch on the Client Side.
I should do the POSITIVE control and make sure I can link up like for like as well.