Coming up with more creations should not be too difficult compared to writing an in-depth storyline. Using the Shaper ending would easily force the plot to go in a different direction. You might find it "boring" but I feel it opens up a lot more avenues than the others.
On the Shaper ending, my one disappointment is that I'd prefer if Ghaldring lives, because he has more character to be developed there after so much lead up in GF3. The endings can pick and choose from various fates and not be one particular ending but a mix.
Going with the Rebel ending pretty much ensures more of the same in GF3 and GF4. This time the creations are bigger and tougher, but then where do we go from here? What climactic thing can possibly be done here to keep the storyline exciting and new? We already have the Unbound, another indestructable creation really doesn't seem all that satisfying. I'm sure we can come up with other superweapons too, but ultimately it's just more of the same.
As I've said, the Geneforge rebellion has pretty much reached a logical cumulation with the Unbound. You can't really build on top of that, but you can build sideways.