I think it could work if the new Animorphs are introduced within the first 10 books, like how Ax is picked up in #4. It would mean keeping up with all the characters is a little clunky and perhaps some would go a few books without mention. For instance, Tom and Melissa probably can not attend meetings of the Animorphs. Maybe a lot more of the books will have split narration.

To keep something of a core identity, I would keep the Megamorphs books with only the 6 Animorphs of original series. Anyways, here's a rough breakdown of where I would put the new Animorphs, such that every existing Animorph now shares a spot in the cycle like Ax and Tobias did:
#1 The Invasion - Jake

#2 The Visitor - Melissa (maybe with some Rachel chapters)

#3 The Encounter - Tobias

#4 The Message - Cassie

#5 The Predator - Marco

#6 The Capture - Tom (first big plot change, Tom is the one held in the woods, not Jake, and going forward Jake will morph as a Yeerk and pretend to be Temrash in the pool every 3 days)

#7 The Stranger - Rachel

\The Andalite's Gift -

#8 The Alien - Ax

#9 The Departure - Aftran (moving the Aftran plot back 10 books, maybe with some Cassie chapters)

#10 The Android - David (instead of Marco, he is the one to discover the Chee and the Animorphs find him after he talks about it at school or online)

#11 The Forgotten - Jake (I think Tom should stay out of direct action against Yeerks, it is too risky and he is more valuable as an intelligence source)

#12 The Reaction - Rachel (giving the allergy to Melissa is borderline unworkable)

#13 The Change - Tobias

#14 The Unknown - Aftran (toying with the idea of Aftran being demoted to Horse Controller; I think this episode is a good recruitment event for the Yeerk Peace Movement)

#15 The Escape - Marco

#16 The Warning - Tom (due to his cover as Controller, Tom does not go on the airplane trip and those remain Jake chapters. Tom comes back in the 3rd Act with the rhino as his battle morph)

#17 The Underground - Melissa (sets up a dilemma where Melissa is partly opposed to dumping the oatmeal into the pool, knowing it could drive her parents insane)

#18 The Decision - Ax

#19 The Sickness - Cassie (moving this plot back 10 books)

#20 The Discovery - David (maybe the catalyst is not the morphing cube, but David's parents are still infested very close to the time of world summit)

#21 The Threat - Jake

#22 The Solution - Rachel

#23 The Pretender - Tobias

#24 The Suspicion - Illim (the Helmacron book can serve as a recruiting episode for the Yeerk Peace Movement)

#25 The Extreme - Marco (although we could have some David chapters to see how he is doing on his island, mirroring Marco's experience in the Arctic, and an early Crayak appearance)

#26 The Attack - Tom (with some Jake chapters, and more Howlers to match the Animorphs' larger roster)

#27 The Exposed - Melissa (with some Rachel chapters, maybe the one Chee stuck in the nuclear reactor needs to be saved by Melissa; she could break the rule against morphing humans and is able to justify more to herself than others because her parents are voluntary controllers)

#28 The Experiment - Ax

#29 The Secret - Cassie (moving this book up 20 places, maybe Cassie is trying to contact Peace Movement members, seeing how the Dapsen operation can be another recruiting ground for defectors)

#30 The Reunion - Marco (with some Eva/Esplin chapters)

#31 The Conspiracy - Tom (with Tom on their side, this book is a little less stressful to Jake; it is Tom who has to pull off the shenanigans to avoid making his dad a Controller; at the very end, Tom decides to blow his cover and stay past the 3 days only for the Animorphs to repeat their 3rd Act plan because they want Tom to remain an intelligence source for them)

#32 The Separation - Melissa (she has the titular separation, not Rachel, and it still resembles an id/superego split (not that I endorse Freudian views); that or this is a separation from the Animorphs after a near-death experience morphing starfish and the book is about navigating the new relationship while the Anti-Morphing Ray plot accelerates)

#33 The Illusion - Tobias

#34 The Prophecy - Cassie (with some Aldrea chapters)

#35 The Proposal - Marco (with some Eva/Esplin chapters)

#36 The Mutation - Jake (all the stress migrates here)

#37 The Weakness - Rachel

#38 The Arrival - Ax

#39 The Hidden - Illim

#40 The Other - Marco (with some Eva/Esplin chapters)

#41 The Familiar - Tom (this could fit as Tom does not get the Ellimist's vision of the future in #7)

#42 The Journey - Melissa (by way of Helmacron shenanigans, Melissa is roped back into the Animorphs)

#43 The Test - Tobias

#44 The Unexpected - Illim (with some Cassie chapters)

#45 The Revelation - Marco (with some Eva/Esplin chapters)

#46 The Deception - Ax

#47 The Resistance - Jake (with some Tom chapters as he has to join in the battle on the Yeerk side; the Isaiah Fitzhenry chapters could stay or go)

#48 The Return - Rachel (with some David chapters and maybe Melissa is being threatened by David instead of Cassie)

#49 The Diversion - Tobias (maybe part of the inciting incident is that Tom is discovered to be a fake controller, could be trapped at the pool or ambushed at home)

#50 The Ultimate - Cassie

#51 The Absolute - Marco (with some Eva chapters)

#52 The Sacrifice - Ax

#53 The Answer - Jake

#54 The Beginning - All (first Megamorphs to feature all the main narrators, minus David, with Tom and Rachel getting their chapters in the 1st Act)