I think it's way past time to re-evaluate just how bad-ass we think the Reapers are.
1) Reapers are not that hard to kill conventionally. We see it multiple times in ME3. Granted it takes a lot of ships and firepower, but it's doable. Even a sandworm can take down a Reaper!
2) Reapers are not that smart. Sovereign really impressed me with his first speech in ME1, but at the end of the game he chooses to fight Shepard by proxy through Saren's body. Why not just vaporize the Presidium? Just idiotic. In ME3 they're made even dumber with the discovery that they're just tools of the Starchild to do his bidding--ie they have no mind of their own, just really deep voices.
3) Reaperized ground troops are a joke. In ME2, Harbinger with any entire force of Collectors couldn't defeat Shepard and his small crew. In ME3, in just one weekend challenge, the multiplayer community was able to slaughter 1 million banshees, 2 million brutes, 5 million everything else. In two days! I myself can kill a banshee single-handedly in 10 seconds with the right kit in platinum multiplayer. So there will absolutely be no problem to retake planets that Reapers control while hiding in space.
I think it is you who needs to re-evaluate how bad-ass the Reapers are.
1) We see it exactly 7 (counting those cannon things in London which I don't think are actual Reapers) times in the ME3. One of those times (the only time We actually see a capital Reaper ship die) it was Leviathan who himself is leagues above everything in this cycle. The other times it are the comparably weak ass destroyer variant of the Reapers and as you already said for one it took an entire quarian fleet to take it down and another one was killed by giant sandworm and not anyone of the council races. That makes a stunning kill count of 5 for the alliance and allies. With vague codex entries which mention some Reaper casualties we can probably say this cycle killed maybe about 5 dozen Reapers (if we are generous). And the Reapers number at least more than 200 capital ships alone(counting only those we see approaching in the end of ME2) but more likely in the thousands considering that they were around for millions of years.
So yeah I'd say that they are hard to kill conventionally and everyone in game even agrees with that assessment.
2)True that, they don't act smart. Because they are the villains and extremely powerful. If they acted smart just once it would be game over and everyone dies.
But since this is a video game they have to carry the idiot ball in order for the player to be able to actually win. (Not solely a video game problem, it happens in other media quite often as well)
Also the fact that Starchild actually controls them does not suddenly negate the fact that they are technoogically superior to everyone else by far.
3)Shepard is a video game protagonist. S/he is and his/her crew are ridiciously overpowerded badasses (with plot armor to boot in Shepards case). Most normal soldiers aren't and to them Reaper groundtroops are a pure horror. That's one reason why millions of deaths happen on the battlefields daily in ME3. And even if it was as easy to kill them as you think, there would still be the Reapers themselves who can vaporize entire battalions in seconds. So no retaking planets is quite impossible.
Also, multiplayer gameplay as example of how Reapers are weak lorewise? Really?