At the end of Mass Effect 3 The Catylyst reveals that it is the creator of the reapers. According to The Catylyst it created the reapers so that synthetics wouldn't destroy all organics and has the reapers commit genocide every 50,000 years. Since you've been fighting the Reapers who were created by The Catylyst he's been the real enemy through all 3 games. So know here's what I don't understand. Why introduce him in the last 5 minutes of the game. First I'll list everything we know about the Catylyst.
1. He created the Reapers who in turn built the citadel and the mass relays. 2. For possibly billions of years he has been overseeing the brutal genocide of 1000's of organic civilizations. 3. Whoever created him is unkown and his origins are a mystery. 4. It is unknown exactly what he is.
Since The Catylyst is your true enemy it would make sense to at least allude to him in an earlier game. Which is where the problem comes in. In the first Mass Effect we knew the enemies were the Reapers and weren't given all the information about them. Then the second game brings in Harbinger who is the main enemy of the second game. By playing Mass Effect 2 it leads you to beleive that Harbinger is your main enemy with no mention of The Catylyst at all. This in turn leads to the idea that Harbinger who taunted and fought you all threw the second game is going to be the main enemy in the 3rd game. Yet the only appearence he makes is in the final push to the beam and then your real enemy is revealed in the last five minutes. There was no mention of The Catylyst in any of the other games. Since he was the main enemy it would have made sense to drop some hints in Mass Effect 2. The only reference we get before then is when the VI on Thessia says that there is a higher force controlling the reapers. Other than that there is no reference to The Catylyst before the last 5 minutes of the game.