Prothean stasis chambers seem to have a tendency to cr@p out after a century or so unless you divert power from others to keep 'em going 
Wrt to Ilos, they did what they could with the resources at hand in the midst of a reaper invasion. They seemed to have some inkling that the available power might be inadequate, as they left Vigil with the programming to manage power utilization. But Javik's pod supplied adequate power for 50K years, so the technology was available.
THe quarians were hanging out on their ships for three hundred years because the COuncil wouldn't give them a planet to colonize
The quarians' delicate immune systems would eliminate a lot of planets suitable for other species.
I understand, but continuing may be a strong word. MEA is not, strictly speaking, a sequel. If it is, it is only in the sense The Lord of the Rings is a sequel to The (Quenta) Silmarillion.
I recommend looking at it more as a brand new IP than a Mass Effect game. I'm not sure they should even have called it Mass Effect, but they were bound to.
That's my take on it as well. I view the trilogy as its own package deal, independent of MEA or anything else that might follow.
And I'm glad for the change of venue. They could not base another game in TMW without somehow overwriting something - canonizing or nerfing the impact of some decisions, handwaving the ending slides we were shown based on the decisions made in that playthrough.
I can continue to enjoy replaying the trilogy knowing that the choices I make, the interpretations / conclusions I draw from the ending, any headcanon I create about what happens next is safe. It will not be overwritten. To me, that means the trilogy will continue to have value, value that may be lost if it were overwritten with new material in TMW.