Did no one else have a problem with the "Think it and it appears" plot point in one of the later books (it's been too long to remember which one)? That seemed like an Ass Pull to me at the time.
Philotic physics was a bit of Applied Phlebotinum that fit well with the already-established canon. In the Enderverse, Philotes are the smallest fundamental building block as well as the physical (metaphysical?) expressions of will. The idea is not "Think and it appears", it's "Find your way to the unplace where philotes come from, and any pattern real or imagined will be adopted and replicated by the infinite unassigned philotes floating around Outside". For instance, no one could even go Outside in the first place before a philote that controlled a powerful enough mental system (Jane) could adopt the complex patterns of people and ships into her own philotic being. Likewise, Ela couldn't simply think "I need an organism that will perform functions necessary to the Lusitanian flora and fauna without killing humans", she had to plot out the bacteria's physical structure exactly and hold it perfectly in her mind for the philotes to assume that form.
Lampshade Hanging Quara wonders the same thing: "This whole solution seems awfully miraculous to me." (So, in short: yes, we did, and I think we were supposed to.)
As Valentine puts it: "It would be too idiotically convenient if the universe could be manipulated this way". It was a rather anti-climactic way to end the two major conflicts, even if it did introduce new problems.
I was reminded when reading on Genius Serum: "[I]t becomes a major concern of the piqueino species that their intelligence is simply the byproduct of the descoloda virus infecting their world. This especially when the human scientists figure out a way to make a non-lethal version of the virus that would allow the piqueinos to safely leave their potentially doomed planet." Now, the point of that subplot might appear to be 'The descolada is the thing doing the thinking', which would be a valid concern (especially if someone tries to use it as a way to make a treaty with it), but... I feel tah they ignore that the descolada is responsible for their intelligence: the piqueinos AS THEY CURRENTLY ARE is a result of the virus. Without it, they would be just another ruminate species that occasionally searched for grubs near tree roots.
