The reason geth lore changed so much is simply due to the fact that their writer stopped writing them. Chris L'Etoile wrote the entire ME1/2 codex and Legion in ME2 with one major exception. The Legion/Tali confrontation scene is not his work. Chris' version was cut for being far too long. If your interested in the general direction he wanted to take the geth here is a quote from him ( three and a half years after he left BioWare )
I agree that Reapers should require quite a bit more to bring them down. During ME2's production, I had a vision of an ME3 scene in which the quarians have to ram a Liveship into one to cripple or kill it. The only thing that would have saved the quarian fleet from destruction was the geth using a wormhole to jump in one of their great works - if not the actual Dyson Shell, then a Matrioska Brain. It throws back the Reapers by chucking black holes at them - biotic-style Singularities on a massive scale.
But if I may borrow the caveman analogy, what you're pointing out there seems to me less that our tech make equivalent units unbeatable, but that our tech allows new types of unit. The Reapers have no equivalent to armor and artillery in that analogy, and I think if you run a bunch of angry cavemen at one guy with an assault rifle and kevlar, he's going to take out a bunch before they reach him, but there's a good chance one is going to get up close and bash his head in with a rock.
Unfortunately, no ever really sat down and worked out the tech base of the Reapers. We just decided a few things they could do, and aside from that, it was "same as us, but better." Their most obvious advantage is in power generation and the size of their element zero cores. They can make crazy-powerful mass effect fields. Kinetic barriers you can't crack. High speed travel. They can cancel maneuvering stress and make high speed turns with a battleship that other races couldn't pull off with a frigate.
But there's another factor overlooked here - and they may have overlooked it in ME3. The Reapers control the mass relays. They knew when they were used, and when they wanted, they could lock them down or set them to misfire (as the Omega relay). I have to use an extended metaphor for this, so bear with me. Take World War I Europe, before the advent of air transportation. There were trucks to drive people around quickly, but most strategic troop movement and commerce was via train. Imagine someone invades Europe and somehow takes all their trains away The tracks are still there, and the invaders can use them, but the defenders have to make do with trucks like this. There aren't as many of them as they need, and they're not efficient for long hauls, because - hey, that's what we have trains for, right?
I thought what normally happens in a Reaper sweep is they lock down the mass relay network. They can focus their forces - few but immensely powerful - at will, while hobbling the mobility of their enemies. They can jump around enemy force concentrations, hit 'em where they ain't, and take out their forces once they're weakened by lack of supplies. It's Pacific War island-hopping on a massive scale - take out the important targets and leave the rest to "wither on the vine." I imagine that in this cycle they couldn't do that because they haven't managed to get control of the Citadel. At least that's how I'd have explained it - though if I were the Reapers, I'd also have had a backup system.
Oh, and W/R/T cleansing the entire galaxy, I've explained a bit of that before. For most races, they know where they are because they use the mass relays. Every time you activate a relay, it's like saying "Voldemort" or tapping a spider's web. You just told them exactly where you are. For races that don't use the relays, they just listen for them. You don't need to check every single planet or system. Just stop every 100-200 light years and listen for the electromagnetic signals that indicate technological life. Yes, that still takes a while, but they have machine patience and probably fleets of drones to help. Any race that doesn't emit technological signals... they don't care about them. Too primitive, no threat, not of interest.
First the Reapers destabilize the defenders by using Indoctrinated agents to set the biggest powers against each other before they arrive. Then shut down most interstellar mobility when they take an active hand. They don't really need to devote time and effort to making better guns. Things went badly awry this cycle. I think the greatest plot hole here isn't that the Reapers don't have sufficiently high tech, but that they didn't seem to have any backup plans.
This doesn't mean that no one ever escaped the Reapers - fled into space far from the relays, made as little EM noise as possible, pulled the blankets over their heads and hoped the monsters went away. As cironian points out, Indoctrination would get a bunch of those. But some would make it. I had a vague idea that the gas giant with structures in it from ME1 could be such a race. And in my opinion, that might make a good opening for Mass Effect 4 - an organized search to find the First Ones and get them to rejoin galactic society.
Only the first part is relevant to the topic, but I thought it was important to leave the rest in. Chris used to post stuff like this almost every other day on the old forums. The other writers did some damn good work here and there, but Chris was operating on an entirely different level.