A 50000 year headstart on trying to decipher it though... I really can't believe that we wouldn't poke around with the relays and figure them out in that time. The Protheans did with less time, and Aethyta talks about building relays so the asari at least must've done some research into them even if they've not got that far (or at any rate it suggests, even if it doesn't prove, that the idea has been entertained).
The protheans also had some very large advantages the way they could communicate. Transfer complete knowledge from one person to another though touch.
Despite the advancements the Reapers still defeated the Protheans even though they were in all likely hood more advanced then current in game cycle. Given that fact the only Prothean artifact left would have been on Mars. With the Reapers harvesting all the other species that relied on their data to advance.
Lets also not forget the only reason game cycle has a chance against the Reapers is because Sovergin dropped the ball. Not only alerting a few people to their existance. Thus making is so they are not caught completely by suprise that they exist. But prevented the Citadel with all that data from falling into their hands until well into the invasion. But after his destruction giving access to reaper tech closing that gap they had.
That Thanax cannon that they use to destroy the Collector ship only exists because they salvaged and reverse engineered Sovergin's main cannon. Giving them access to fire power previously unheard of.
With the chance to correct the issue the Protheans created with the signal the Reapers would be free to invade and attack in their standard method of complete and utter surprise crippling the command structure and isolating systems. Allowing them to pick them off system by system.