Considering the number of habitable planets in the galaxy, terraformed into that condition or otherwise, the damage inflicted to one in the course of a Reaper harvest (one world in ME2's galaxy map is described as being bombarded to the point where only bacteria survived), and the time it takes for intelligent life to evolve, 50,000 seems like far, far too little time between cycles. Hell, count in the damage done by non-Reaper aliens to various planets (Javik talks about burning hundreds of worlds to contain the Rachni) and I'd be surprised if the galaxy produced a single space-faring race every twenty cycles.
Gotta wonder how often a Reaper cycle consists of their vanguard poking up its head, seeing the Citadel is still dormant, and hitting the snooze alarm.
*lol*
...
But remember the reapers tend to ignore less advanced sentient species and non-sentient life.
It's estimated that there are 100 billion planets in the milky way, possibly with trillions of rogue planets between stars. There could be as many as 40 billion earthlike planets orbiting sun like stars and red dwarf stars (the last is show to be habitable in mass effect, in reality they might not allways be). Still leaving around 11 billion earth analogues around sun like stars.
In the mass effect universe there are examples of life being able to survive space and travel as spores between planets. I'm guessing life will exist many many many places and that means a relatively high chance of intelligent life appearing.
If we go by the number of 40 billion planets and suppose the reapers attack an average of 1000 planets each cycle that leaves room for 40 million cycles over 2 trillion years. Ten times as long as they've been doing it so far.
If red dwarves a habitable it's not a problem, for while sun like stars only live an estimated 8-10 billion years, red dwarf stars might live for many trillions of years. Perhaps up to 10 trillion years for the lowest mass ones.