Going Rogue adds a new zone (Praetoria), which was initially only accessible to new characters created there. As of the current issue, it is now possible for existing characters to travel to the new area.
As for effects for existing characters, provided that you have the expansion all existing characters will gain access to the alignment system which allows characters to change alignments ranging between hero, vigilante, rogue, and villain by completing missions with an associated moral choice (tip missions / morality missions).
If you have the expansion, you automatically gain access to the new powersets, but be aware that much of the content added is in the new zone, so you will either need to start a character there, or move a character there. Praetoria currently (issue 19) has only content in the lower levels (up to about 20) after which point you move to Paragon City or the Rogue Isles.
Finally, to access the new post-50 content (the Incarnate system, which includes additional buffs, and level shifts) you must have going rogue. This applies to both new characters and existing characters.