^Problem is that all the prothean's plans were ruined by indoctrinated agents and the Ilos team only survive because of luck and even then maintaining cryo for centuries is difficult due difficulties in power management. The Ilos team once started with hundreds maybe thousands of individuals but at the end there were only six individuals left since vigil had to divert power from most of the cryo pods so logistics does play a major factor in this and planning for it means leaving no room for error as the smallest of mistakes could ruin everything.
Indeed there are issues but it's not impossible
Ilo was a planetary based suspended animation base which would have required them to lower or shield energy output from detection to ensure survival via secrecy.
Eden the planet Javik was ultimately found on failed because of an ongoing attack after being sold out by indoctrinated soldiers and was under attack but then protected by detonating a Neutron bomb to decimate all organic life if I remember the mission properly.
The colony ships could in theory work...
On Ilo, Eden, and Thessia they had Prothian VI capable of identifying indoctrinated life forms which in theory could have worked as gatekeepers for evac ships that would take colonists to long distance evac ship(s)
If there were multiple ships, every ship would act as an independent cell from the rest, no ship would know of a 2nd ship ever.
To protect all of the ships, a dummy ship with "volunteers" would be sent out with X number of agents being sent out with the knowledge of that one ship being the life line & knowing the trajectory used to divert the attention of the reaper forces for just long enough for the other ship(s) to escape the galaxy.
Once the other ship(s) are out of the galaxy they could fully utilize their power plants aboard the ship to put the crew into stasis and then hand over keys to the course to the on board VI which would then plot a course into the next galaxy & locate a habitable planet for its crew.
Fast forward 40-50 thousand years with the evolution of the species as a whole and technology you would have many many Prothians really really PO'd at the legacy they were given to eradicate the Reapers and reclaim their home.
Yep I know I know it almost directly reflects the story of the Geth vs Quarians on a much larger scale.
Potential downfalls
Any number of hostile Races could find the Protheans or data left behind by them and want to claim our Galaxy or enslave and exploit the Reapers for their own gain
All ships failed to get to habitable planets before the crew perished leaving the VI floating & possibly returning as is or evolving into fully fledged AI
Protheans come back and after finding Reapers "Controlled/Destroyed or Organic life turned Hybrid" they could try to reclaim their planets by force to eradicate the remnants of the Reaper forces and the Alliance that completed what they could not.
Protheans come back to our Galaxy with Military might and attempt to return to their seat of power to rule how they ruled the previous cycle, deeming the lesser species worthy of being within their alliance.
Potential outcomes if the Protheans return
-- Javick is seen on the Extranet and just before he can commit suicide his people find him and beg for his help with trouble in their galaxies. -- If Javick is dead they'll head to the citadel as it's being rebuilt. -- Queue the Remote galaxy exploration, politics, growth of Military might.
-- Mass Relays opened up for full galaxy exploration and a new relay between the Citadel and Galaxy X to allow more Protheans to make the trip easier between galaxies
-- Yahg given space flight by Protheans either intentionally or via a crashed ship onto the home planet of the Yahg -- oops
Or if what I saw several months ago stating that the Reapers were in fact attempting to force an evolution fast enough to stop a cataclysmic event through destruction and conflict. We would now be attempting to stop the "Big Crunch" aka the opposite of the "Big Bang" where the universe would be collapsing into a single point in space to become a new big bang & reboot the universe.