Just a few info tidbits to throw in:
1.
The Reapers fear humanity. Listen to Harbinger's Big Bad speech at the end of ME2, that's not a "reason you suck" speech, or evil gloating: that's a genuine paper tiger "oh shit" moment.
Sovereign went down swinging and boasting. The Reapers want humanity out of the way
right freaking now. It makes sense they'd drop the hammer on Earth, and hard.
2. The Reapers' main weapons are surprise and overwhelming intelligence and logistic advantage. Hitting the Citadel first gives the Reapers information on every galactic civilization, level of technology, location and disposition. Plus, they can rely on Indoctrinated sleepers, control over an (if present) galactic communications network and locking out the relay network to non-Reapers.
2a. Word about (and proof of) the Reapers is going to spread. A Council race's homeworld getting genocided isn't exactly something that can be kept quiet. The
SR-2 has a Reaper IFF, which can be reverse engineered just like Reaper weapons, armor and shield tech. The Reapers probably don't have much solid intelligence to work from, considering their best intelligence assets were a lone Turian spectre, Geth heretics, and a few decades surfing the extranet.
The biggest secondary threat are going to be the billions of humans who'll probably end up Indoctrinated before Shepard can do his/her thing. Remember, the Reapers can do that
fast if they don't care for the usefulness of said Indoctrinated. Oh, and TIM who I've thought has been Indoctrinated or has his own Reaper-related plans from step 1 (seriously, why would he want a Reaper factory?).
3. The Citadel races are growing technologically out of the Reapers' control. The Geth already don't rely on Reaper tech. The Citadel races
reverse engineered a Reaper and used data from the Sovereign battle to upgrade what wasn't reverse engineered. Check your ME2 codex, where do you think the armor, shield and weapons upgrades came from?
4. The human fleet at the battle of the Citadel was one fleet out of several. Of the
fourth largest navy in the known galaxy. Again, check your ME2 codices: the turian fleet dwarfs the humans', and that's in the happy-shiny-people
Paragon ending of ME1: if you let the council die, you've effectively launched an arms race between the Council races. God only knows what the
salarians have squirreled away in the ass end of nowhere.