Actually though Az, thinking about it long and hard...
One could argue that part of the problem with the Wolvie arc was that
so many mysteries were introduced that there could
never be a satisfactory resolution. Same goes for Lost, etc.
Sure, a game like this positively
thrives on GM and player interpretation, but that, perhaps, is a trick that only works for a while (look how fed up some people have evidently become with Lost: same thing can surely happen with SR- it just takes longer because there're such long gaps between 'episodes'.)
So I guess what I'm saying is... if, ultimately, you feel you've been strung along and the designers of your favourite fantasy had no great coherent picture in mind when they started it... sooner or later that's going to bite.
On the other hand, I do believe that- even with a 'history' as convoluted as SR, it
is possible to construct a perfectly valid 'solution' that fits the available evidence, while at the same time opening up new questions and new mysteries. That- actually- is the wonder of science, as far as I'm concerned!
Sorry James McMurray, BTW, for perhaps distracting from your point. For what it's worth, I'll reiterate that I believe that the Great Pattern was a form of early Matrix, therefore the magical happenings that occur in the Matrix occur as a result of a resonance between the Matrix and the Great Pattern.
I do believe that a magical entity could, with the right portal, enter the Matrix, but I also entertain the possibility that a Matrix entity could, with the right portal, enter the magical realm (which interests me rather more what with the parallels between AIs and Passions)
Furthermore the Matrix 2.0 might have been engineered (by someone- I'm not saying who) to better reflect the Great Pattern and therefore to draw the two networks closer together.
Let me also say that I believe metaplanes to be the Great Pattern equivalent of Reality Filters, and that the materialization of Spirits in the physical realm might resemble a sort of ancient hologram/sologram technology that is now fundamentally built in to the Earth and its life-forms.
I also believe that the Gaeacentric view of the manasphere is false (holding as evidence the fact that Foveae have life but apparently not 'mana'), and that 'raw mana' is in fact present throughout the universe (to the delight of horoi), with Earth being perhaps the only exception on account of the Great Pattern acting as a sort of Firewall + Operating System of threaded mana that thereby limits Horoi abilities.
I furthermore maintain that the cycle of magic is not a predictable clockwork mechanism (compare your time-scales folks!) but rather a case of the Great Pattern 'rebooting' now and then.
To actually answer your question, I'm much more worried about AIs finding a way to turn themselves into spirits than spirits/mages finding a way to turn themselves into AIs. But then I believe that Deus is the re-emergence of Dis and Mirage is the re-emergence of Mynbruje.
Still, I think it's all pretty much inevitable and lays the way for a pretty interesting Epoch Seven, about which I may post some other time. And if you read through all of that, here, have a banana!

By-the-way, I am the Grand High Poobah of the Secestry of El, and may therefore not constitute a credible witness.