... As far as we know. I havent seen anything official on this yet, so:
For an extreme example: say Rebellion gets all the new stuff integrated and balance, except for scouts. well, then it wouldn't have scouts. its something thats in the original and not in Rebellion (in this hypothetical case). One thing I would expect to definately change would be research trees; some things will probably move a bit or be removed. Envoys potentially will be removed or greatly changed.
Bottom line is that we dont know what will be in Rebellion. Most of it should be very similar to Trinity. Some of it will be new. how much will cross over and what may not are not known at this time.
What we do know is that vanilla Sins, Entrenchment, Diplomacy, and Rebellion each have their own executable. so, if Rebellion does not include vanilla sins, entrenchment, and diplomacy; you will not be able to play those without grabbing trinity. If it does include it, then you can.