I don't really have any ideas as to what IS chasing them, I'm just really tired of all the morons on the ME3 Bandwagon going "zomg its teh reapers lolololooololo!!11!!!ELEVENONE!1!!!"
Anyone and everyone should be able to tell that the reapers wouldn't stand a chance in this universe.
Capital Ships and probably Cruisers are bigger than the biggest of reapers. They have infinitely more powerful shields and weapons.
Advent beam weapons would cut right through them, TEC Gauss rail cannons would blow them to bits, Vasari pulse beams and nanotechnology would also get rid of them easily.
Not to mention the Titans, ranging between 15 to 25km in size, depending on which Titan, and Star Bases, which are larger than the Titans.