True, we're seeing less of Twilight now, seeing as she's reached her original 'endgame' which ended up being her transformation into a princess. The CMC have their marks, and Rainbow's about to get Wonderbolt status. It looks like mission complete, right?
Take a look at what Writer's Digest Editors claim in "Creating Characters: The Complete Guide to Populating Your Fiction"
A character needs to have four things:
1. external motivation (what they want to achieve)
2. internal motivation (why they want to achieve it)
3. external conflict (what's stopping them from getting it)
4. and internal conflict (what they're willing to do to get it)
If Twilight's story, or anypony's story is going to see a "Chapter 2," she'll need a new goal, a reason for getting that goal, a visible threat, and a conflict of identity.
She, the CMC, Rainbow Dash, and anypony else reaching the end of their "Chapter 1" could very well see the start of a whole new adventure, and as long as its an interesting adventure, people will want to watch it unfold.