We're not decided on that yet - it's perfectly possible to do either, as the routefinding code we have in the library will let us determine if one asteroid is linked uninterrupted with another by asteroids of the same owner.
Waypoints (like in Starcraft or similar) are still probably the best solution for that. No need to invent a wheel when it is already invented

I look forward to see how you guys will solve this problem.
I don't know exactly how the other solutions suggested in this topic will work to solve the problem (bridges direct the movement of the newborn seedlings, but what about regrouping and merging groups together?). Different dyson tree structures are a nice idea to bring more diversity into gameplay.
Tracking seedling types (and maybe separeting groups of seedlings based on characteristics)? Very cool idea. I'm all for that. Dividing group with fast and weak seedlings and slow but tough seedlings into two groups will be very useful.
Also please don't add
a sun into the game universe. "Sunfree" or "sunless" universes with life are rare and will help to differentiate this game from others. Evolution of the different dyson organisms will be very interesting.