The Reapers because they could probably find a way to control some/most/all of the transformers in a similar way that they have controlled the geth. I mean, I'm not a big transformers buff, so if I'm missing something let me know...But that's my answer. However, if just on brute power/force...still the Reapers.
Looks like it's pretty one sided, I'm going to say reapers, because they can blast the transfomers too death from 200-2000 kilometers away, and have sheilds and a hull capable of withstanding constant fire from a kilometer long, 1,000,000 ton (I think) dreadnought and destroy an entire fleet by itself no problem. alternativley it could land and stomp the transformers to death: transformer < 2 kilometer starship. Also there are thousands if not millions of reapers.
Only advantage I can think a Transformer MIGHT have over a Reaper is the species ability to read, decipher, and perhaps even alter data codes and signals. Transformers could potentially be immune to indoctrination and if done right, possibly even turn the code against the Reapers. But in a full out no holds barred fight, a single Reaper would devastate a group of Transformers. A Transformer might have a bit more of a chance of fighting a Reaper also vs us organic based life since every cycle, the Reaper's primary targets were organics as they tend to be able to manipulate synthetic life rather then fighting them.
Humans already proved that a Transformer can be hurt by a simple railgun. Well, the reapers have weapons orders of magnitude more powerful than the megajoule range railguns we're working on now. It wouldn't even be a fair fight.
Reapers for sure. The Transformers do have the benefit of stealth as they could be something easily hidden like a mobile. But the fire-power of the reapers would destroy them in minutes. Could we even see indoctrinated Transformers?
Reapers created a code that overrided the Geth and turned them onto their side. Transformers have shown us they can hack the US Military in the movies.. I'll take rewriting an entire synthetic species as evidence they're the superior ones.
Reapers vs. Transformers is kind of like Godzilla vs. Bambi. Is this even a debate, really?
A single reaper (in the first ME) took a tremendous amount of combined effort to fight, and destroyed a third of the entire Alliance warships. Heck, the entire galaxy sent their fleets (ME3) and still were losing until you destroy/control/combine the reapers.
Maybe the Reapers would make Transformer-Reapers, though...
