Although clearly technologically superior to the Citadel forces, the Reapers have experienced casualties in the battles across the galaxy. This indicates that, theoretically, with the right intelligence, weapons, and strategy, the Reapers could be defeated.
Unlike the mass effect relays that they created, Reapers do not have quantum shields. Locking itself down at a quantum level would leave a Reaper unaware of its surroundings until the shielding deactivated. Instead, Reapers rely on kinetic barriers.
In the case of a Reaper capital ship, these kinetic barriers can hold off the firepower of two dreadnoughts simultaneously, but three clearly causes strain, and four typically results in destruction. Weapons designed to maximize heat damage, such as the Thanix series show better results against the Reapers than pure kinetic impacts.
The barriers of a Reaper destroyer are less formidable than those of a capital ship. It is possible for a single cruiser or many fighters to disable or demolish a destroyer if they can get within range before they are themselves destroyed.
The Reapers' energy sources are not infinite. For example, to land on a planet, a Reaper must substantially reduce its mass. This transfer of power to its mass effect generators leaves the Reaper's kinetic barrier at only partial strength.
Sovereign was destroyed while assuming direct control over Saren. The feedback from Saren's death seemed to entirely overload Sovereign's shields. Current Reapers do not seem to suffer from this design flaw.
Reaper capital ships can turn faster than Citadel dreadnoughts, but to do so, they must lower their mass to a level unacceptable in combat situations. Consequently, it is possible for a dreadnought to emerge from FTL travel behind a capital ship, then bring its guns to bear faster than the Reaper can return fire. This is a poor tactic, however, against Reapers flying in proper formation.