I think part of the issue was that while the Reapers were advanced, they were at a distinct disadvantage because of the Protheans in the previous cycle.
Sovereign was supposed to activate the Citadel and let the Reapers through, but the Protheans fucked up his plan, so when the races of the galaxy reached the point where the Reapers would normally begin harvesting, he sent his message only to have it ignored. So Sovereign had to come in and open the gate himself, which took many more years and let the races continue building towards where they could start putting up a fight when the Reapers finally arrived.
On top of that, Sovereign was subsequently foiled, and his wreckage was used to create several more advancements in technology. The Asari even admit in 3, I think, that they have the technology to build new Mass Relays, it's just prohibitively expensive for them. AND things like Dreadnoughts and multiple ships were proving capable of taking out Reapers, so the galaxy was winning battles.
The problem was that they weren't winning enough of them, but the Reapers did take not-insignificant losses during 3 (and if you don't pick a colour at the end, you still get Stargazer, so presumably they were too weakened to be a serious threat any more).
And on top of all that, they were opposed by Shepard wielding the Upper Left Blue.