MeshCore or Meshtastic - which should I choose?

Both are excellent. Choose based primarily on what your local community already uses. Don't pick a protocol solely on technical merits (routing efficiency, encryption) if it means being alone on the mesh - community presence matters more.
Choose Meshtastic if:
Your local area already has an active Meshtastic network
You want the largest app ecosystem and community support
You want the most beginner-friendly experience with polished apps
You want the widest hardware compatibility
Choose MeshCore if:
Your local community uses MeshCore
You are building dedicated repeater infrastructure
You prefer MeshCore's selective routing model for direct messages (both MeshCore and current Meshtastic use public-key encryption for direct messages; neither provides Signal-style forward secrecy)
You are deploying a large network (50+ nodes) where flooding creates congestion
Can they interoperate?
No. Different packet formats and routing protocols. A MeshCore node and a Meshtastic node cannot communicate even on the same frequency. Many operators run both on separate devices for different purposes.
Technical comparison
Feature
Meshtastic
MeshCore
Routing
Flooding
Path-based (path discovery)
Community size
Larger
Smaller, more technical
Hardware support
Very broad
Good (915 MHz boards)
Best for
Personal use, joining existing mesh
Infrastructure, large networks