I could have done without the Reapers. Yeah, it would take some tweaking to make each story standalone, but I think it would be worth it. I'm tired of big trilogies where everything ends on a cliffhanger until the next game. The Final Fantasy games came made dozens of sequels with their own continuities, the Ratchet and Clank games are almost all standalones, why can't we do this with Mass Effect?
Mass Effect 1: A rogue Spectre named Saren has found a way to control the Geth in order to exterminate humans in a genocidal campaign. No need for the Reaper plot whatsoever. You have your primary antagonist and his army of goons right there staring you in the face, no need for a puppet master.
Mass Effect 2: Aliens called the Collectors are attacking human colonies in the terminus systems. A black ops organization called Cerberus shanghais you and your crew to take them out before they can enact their nefarious deeds. Main antagonist is Harbinger and the Collectors' Hive Mind. There you go again, primary antagonist, army of goons, no need for Reaper influence.
Mass Effect 3: If a game did need to have the Reapers, it would be this one. Since the games already insisted on making the Reapers unstoppable without Space Magic, I would have changed the plot from building a "We-have-no-idea-what-this-thing-does-but-let's-try-it-anyways" device, to trying to discover the Reaper's origins, be they extragalactic, or a super powerful race that has lain dormant for millennium.
The games already have their own antagonists, they don't need some generic robot cthulu aliens to pull the strings every fucking time.