Actually, the best targets for this experiment were still the Dimension Apostles. After all, both are incompatible with the Real World and can only use a portion of their power after becoming stronger. Deities are even a bit better off; at least Tier Four and even Tier Five Deities are compatible with the world.
Combining the two might even neutralize some of that incompatibility.
Furthermore, Isaac had stronger control over the Dimension Apostles, which would have made the process safer and more manageable.
Unfortunately…
In the Endless Tower, although Isaac could still use the power of the Dimension, he could no longer use it as a conduit or summon Dimension Apostles from it.
He was helpless, but what could he do? It was a Great Creation, after all.
