The tracking plan didn't seem to be in place for the Alliance and Earth.
There was.
(Opening cutscene) Hackett: "There's something massive on long-range scanners."
Anderson: "How long do we have?"
Hackett: "Not long. I've sent word. The fleets are mobilizing."
Anderson: "Something big's headed our way."
Shepard: "The Reapers?"
Anderson: "We don't know, not for certain."
Shepard: "What else could it be??"
Tevos: "(...) while the Reapers focus on Earth, we can prepare and regroup."
Also, if the Reapers attacked every home world at once would the Council homeworlds really be keen to lend a hand to reinforce the Citadel? If they bum rushed the Citadel instead of Earth would the organics be able to react fast enough?
Do you understand how relays work? The Reapers cannot "bum rush" the Citadel. There's a limited # of ships that can pour through a relay into a system at any given time, and only few are actually connected to that system (most only go two ways). The Alpha Relay was the one exception, and it got destroyed by our side (one way or another).
One can point out the arrival of Shepard's fleet on Earth for the final battle, but it says more about the accuracy of that cutscene than the Reapers' decision to avoid the Citadel.
Cerberus managed to attack the station and cut off communication, surely the Reapers (who probably have that Collector jamming technology) could do the same thing.
An attack which, per Shep, likely crippled their manpower and resources. The Reapers may be better supplied than Cerberus, but any battle for the Citadel will be costly, even to them. Which brings me to my next point...
Even if they do close the Wards the Reapers would at least hold a vital system.
It's not about the war or strategy to Reapers. It's about harvesting, and the cost-to-benefit ratio. One Reaper is an entire civilization's cultural knowledge and memory. If it dies, it's gone forever. Using them is necessary to carry out the cycle, but apart from that, they must be protected at all costs. You can't replace what's been lost with one.
That's why the Reapers, for all their arrogance/hubris, still have their Citadel backdoor-trap in place to finish the wars before they even begin. In a normal cycle, it's likely that they lose not a single ship, save for maybe a couple flukes here and there.
That's why taking the Citadel can wait for a bit while lowly thralls are tasked with it instead. Couple that with the fact that the Citadel can be shut off from outsiders
All of this also ignores the fact that there is a control panel for the Wards in a place that no one except for Reaper minions can get to. Was there something super special about TIM to make him the only person to sneak down there? Couldn't any dime-a-dozen organic do the same thing even if they did need Reaper implants?
What the blazes are you talking about? Unless you subscribe to IT, which brings about another set of holes into your argument altogether, the entrance of Anderson and Shepard into the same location debunks the idea that there's any such "Reaper-only territory" on the Citadel.
TIM broke through security to the Citadel control-panel because he was powerful (with the Reaper upgrades he had implanted), powerful enough to even kill Shepard and Anderson in a scripted scene (something that very few other characters in the story can boast)!