Okay, I'd suggest two things: Firstly, up the threat of the Reapers. They've been doing this for how many epochs and they can get taken down by a tricked out frigate? No.
Actually a few of the main reasons why the Reapers got messed up by the Normandy was that she never actually punched above her weight class, she is a frigate and had only took down Destroyer Reapers which are basically the Reaper version of a frigate (only with more tentacles), was equipped with a reverse-engineered Reaper main gun, had Joker at the helm, had EDI with a Reaper IFF code installed and one time needed the entire Quarian combat fleet to take one down.
Also like it has been mentioned before, the cycle should have started way before ME1 came about anyway, Nasara had to spend decades/centuries looking for proxies to work behind to figure out why the Reapers didn't pile through the Relay.
The Reapers
intentionally leave titbits behind in order to influence the tech trees of the civilisations in each and every cycle and expect everyone to follow along. It was just that the cycle with the humans was longer than expected, giving rise to stuff like the Javelin missile and QEC, one of the ways the Reapers win is by intentionally cutting off the Comm buoys, no FTL comms mean that everyone they face would either be a disorganised mess or too small to pose any serious threat.
They pretty much took down the Photeans
Galatic Empire doing it this way, all because every space faring civilisation that reaches a certain point in it's expansion would use the Citadel as the focus of their government, which mean they would put stuff like military data and census forms on the Citadels mainframe, meaning that the Reapers knew where the Photean navies were, where they weren't and exactly where to hit.
They built the building blocks to virtually everything that most space faring races in ME have and know all the codes and hacks.
The Reapers were going to be boosted anyway because of Marvel Crazy SCIENCE anyway so it's a moot point.
Basically....the canon!Reapers are in a way the 'Anti-Spiral race' of the ME verse, they are old, powerful, somewhat smart...but most of all, stagnent.
Some fans actually said that 'going for a TTGL ending even if the player knew it was hopeless would have made a better ending'.