Thought I'd chime in with my own opinion & views.
So I'm a massive Mass Effect fan. You may say I'm just a fanboy & that I'm blind & I don't see what's bad because I'm such a big fan. But I just see things differently to most. With many things, not just Mass Effect.
So. Why don't the Reapers attack the Citadel at the beginning of ME3? It's simple. Because the game would be over instantly. In games, stories & fiction, you need to suspend your disbelief. Just allow yourself to overlook something to enjoy the game.
Yes, the Reapers tactics are to attack at the heart of galactic civilization & effectively wipe out most forms of galactic leadership almost instantly. & isolate every system at the same time. Nobody would be able to communicate, travel between systems. Pretty much everybody is screwed & the Reapers have already won. It's just a case of a few centuries of mopping up the dirt. If that happened in ME3 there's almost no way you could make that believable & make it plausible to defeat the Reapers. You simply need to make some exceptions to allow a story to happen.
So when the Reapers arrive in ME3, they don't head straight for the Citadel because things are different this time. Possibly for the first time ever, the Reapers don't have quite the same level of surprise. Sure a few people eventually believe shepard, but most still don't. & the Reapers can't enter the galaxy with the same effect this time. Although, it is still a very big surprise when they arrive. Now, as far as I'm aware, I think I remember reading somewhere not long after ME3 released & some of the devs/writers answered some questions. But I think Either when the Prothean scientists reprogrammed the Keepers to ignore the Reapers commands it also had the effect of stopping the Reapers from directly controlling the Mass Relay system. Example, You no longer have access to your TV remote, so you can no longer turn it off. Your only option is to manually turn it off on the TV itself. That is what the Reapers tried to do with Saren. They used him to Open the Citadel Mass Relay to allow the Reapers to return en mass like their main plan A. & then they would have shut the Mass Relay system down their & then. But that plan failed.
The only way for them to deactivate the Mass Relay system is to send somebody inside & manually give the Reapers access. That is likely what the Reapers tried with the Cerberus coup, although it's never confirmed, it would make a lot of sense. TIM gives his troops the order to take over, TIM doesn't realise he's being indoctrinated, so in his eyes he's doing it to save Humanity, when really he's just becoming another pawn for the Reapers. Like Saren.
In the end, it ultimately won't matter if they don't attack the citadel right away. The Reapers WILL win, that is a guarantee. There is NO way you can defeat them conventionally. It is flat out impossible & it's stated numerous times. I don't understand why people wanted to defeat the Reapers conventionally, it diminishes their power & their fear factor. There are thousands of them & each one is capable of taking on an entire fleet. Look at Sovereign in ME1.
So even if the Reapers don't shut down the Mass Relays or take control of the Citadel, so what? It'll take a little longer. But they'll still win. & that's fact, whether you believe it or not.
Now, eventually the Reapers do take control of the Citadel, by the end of the game. & how long is ME3's timeline? Lets say 1 month. If it only takes one month, & the last cycle lasted centuries, then when you put it to scale the Reapers did take the Citadel instantly, more or less.
The only thing we had on our side that was different from previous cycles, was the fact that our races more or less worked together & we found the plans for the crucible AND actually built it. Sure, if the Reapers had disabled the Mass Relays we wouldn't have got it built, but then we wouldn't of had a game would we? Again, suspend your disbelief, so we can have a game/story to enjoy.
Then comes the Catalyst 'Star Child'. Now, I get peoples frustration with this kid. But I don't get the confusion. He created the Reapers to solve a problem. & he succeeded. Whether you disagree with his methods or not. He's still a machine & he used machine logic, & his solution works. You can't argue that.
So why can't he control the Mass Relays if he IS the Citadel. Well again, suspend your disbelief so we can enjoy a game & story. & yeah, I know you're all going to call me out on that & say I'm ignoring problems. But I'm not, because it can still be explained imo, without causing plot holes.
So, why should he control the Citadel. He's just the AI that created the Reapers. The Citadel is part of him, just like my Hair is part of my body. Do I control when my hair does & does not grow? No, I don't. Sure, I get it, it does seem strange & seems like a plot hole. But c'mon this is all science fiction/fantasy. Yeah, they could've taken more time & come up with something that makes a little more sense. But just think of the Catalyst as being the AI that created the Reapers & embodies the collective intelligence of all Reapers. The Citadel is part of him, but to maintain his secrecy he needs to give up that level of direct control. He can't risk detection just to have control over the station. & why would he need it when he has a fleet of possibly 20,000 Reapers (1 billion divided by 50k. But the cycle wasn't always 50,00 years. & we don't know how long exactly they've been around. But it is at least 1 Billion years, thanks to the Leviathan of Dis) that can do his handy work for him. If the Catalyst can control everything on the Citadel, then the Reapers plan B is unnecessary also. Why send Saren if the Catalyst can just open it up himself? Odds are He's dormant until the Citadel is 'activated' by the Reapers. It could also keep him hidden. 50,000 is a long time for races to go snooping & accidentally discover things they shouldn't. So it's not hard to imagine the Catalyst is very deeply hidden between cycles. He is still a machine after all.
There will always be plot holes, in most fictional stories. But I feel most of these are easily explained & people are too harsh on them.
Personally, I'm happy with the story, events & logic with everything that happened in Mass Effect. Could it have been better? Sure, in some places. But I still loved it regardless.