Leviathan made me feel like the bigger threat has yet to come.
Control: I've never liked control. It's too dangerous in my opinion. Who is to stop some psychotic group similar to Cerberus to build another crucible and for some power hungry crazy person similar to TIM to take control. I won't take that chance. Now with Leviathan around whats to stop them from taking out the now controlled Reaper fleet. They are obviously a patient race and could take them out over countless eons to re-establish control over the younger races. And what do you do about rebuilding a new Reaper...destroy a society?...and the cycle continues.

Destroy: I won't sacrifice EDI or the Geth. Never going to happen. They have just as much of a right to life as anybody or any race. I also see the Reapers as a victim now. We now have a diminished numbers, small surviving fleet, and a looming threat of "What if the Leviathans decide to try to take over again." We don't have the Reaper fleet, the Geth, or our own lovable EDI in this one to help.

Refuse: Yes...let me fail all the people who asked me to save them because I'm too stubborn to put my personal morals beliefs aside to make a questionable decision. Leviathan is the next cycles problem I guess...that's...fair...

Synthesis: Upgrading all organic life down to the molecular level to include technology. Upgrading all synthetic life to have true emotional comprehension and organic understanding. All life is now "connected" via galactic network allowing knowledge and understanding to be shared at the speed of light (similar to the prothean cosmic imperitive, except "wireless") while allowing to completely retain individual personality and sense of self. The downside: These "upgrades" are done without explicit permission from the individual. I think this is the only way to make sure the Levaithans and thier kind have trouble controlling us because of the new upgrades. Also we have a united galaxy from a potential threat and the Reapers fleet, including all the knowledge they have gained over the eons. Granted we already have a way of sheilding their orbs but i'm sure there are other ways. Obviously they didn't use an orb on shepard while she was in the water. Proximity was enough.
The Leviathans are a far older threat that have been waiting for the day the Reapers are gone so they can dominate the galaxy again and be worshipped as gods.
These of course are my opinions and interpretations. If you don't agree with me thats your perogotive.
If, however, you have information to input without acting like a child I'm always welcome to new data or another way of interperating this. A heated discussion is one thing, telling someone's
opinion is wrong is...well, asinine and closed minded.
Who knows what the future will behold though