And removing those from the big Prometheus drones only serves to narrow down the forward arrowhead a little. The thing is already as barebones as barebones can be - almost two-dimensional save for the engine nacelles!
One possibility: because you need combat drones, which by definition have to have large engines and heavy weapons, and you need a crewed control center, which doesn't need either of those but does need to tag along - right until combat is joined. It makes sense, then, to use the drones as "carriers" for the control unit.
It is an engine capable of moving a set of weapons fast enough to catch a starship. I.e. it is a starship engine. Those don't come at the size of a walnut in the 24th century yet. But if they did, obviously the E-D would have them.
Hardly. But such "drones" would only cover an extremely narrow area of warfare; in order to cover any appreciable part of it, you need automated starships, not sessile guns.
No, it does not. Captain Keogh was right to dismiss it as fit only to fight glorified shuttlecraft - it has never stood any chance against capital ships, as nicely evidenced e.g. by "Armageddon Game". It has never even stood a chance against the smallest Jem'Hadar ships, apart from "Treachery, Faith and the Great River" where the first of the titular buzzwords was key to victory.
Nope. Neither the Reaper nor the Gray Eagle has any place in this comparison, as they are not combat drones - all they can do is assassinate helpless victims.
A combat drone, capable of fighting at least its peers (and by your criteria, its biggers), starts out at the size range of X-47. That's a hugely complex machine, only theoretically capable of combat even at its projected operational best, and vastly more expensive to operate than a F-16 category crewed combat aircraft.
You don't get a combat drone by installing a toy aircraft engine or an automobile powerplant. You need a turbojet of credible size. And the Reaper has none, and cannot do combat.
Well, of course not, if they are intended to be incapable of combat. Which is the design goal of all the currently operational flying drones - they are either pure eyes-in-the-sky or delivery platforms for weapons capable of hurting only the softest of targets, with the theoretical ability to hit a moving target now very gradually translating into operational reality. Hell, a Reaper can't even actually shoot down a Reaper despite its ability to carry light fire-and-forget AAMs.
Well the main problem I have with your argument is your overreliance on The Prometheus as your primary basis of what drone warfare would look like in the 24th century. While the full background of that class of ship is speculation, it could easily be:
A) An R&D boondoggle that would never see mass production due to its inefficient design.
B) A design for an existing starship retrofitted to be controlled by computer similar to the way the Enterprise was in "The Ultimate Computer"
C) The Prometheus ship was designed to allow Starfleet the flexibility of utilizing the ship as mainly automated or with a full crew complement and thus built it with all the extra areas that would not be utilized in the automated configuration.
Clearly, the Star Trek universe has shown almost no interest in robots, androids and artificial intelligence other than their sporadic inclusion for storytelling purposes. The obvious reason for this is that people tend not to view TV shows or movies about automated ships exploring space. Its kind of boring. Thus despite our own society moving in that direction its been established that hardly any races in the ST Universe have adopted a heavy reliance on computerized automation to the extent we would expect.
Have you ever heard of the term "apples and oranges"? Comparing 2nd and 3rd Generation drone vehicles with 70th and 80th generation manned aircraft is not quite equivalent. Our current military is moving in the direction of automated system and the Air Force is at the forefront of this. Studies have shown that the same aircraft designed without pilots would have a $2-5 million savings without having to build a cockpit for the pilots and all the other redundant systems necessary to ensure the pilots survival. Additionally, often the limitations of what aircraft can do is artificially lowered by the G-forces and strains that humans can endure while piloting the aircraft. That restriction would then be removed allowing for faster and more agile aircraft which could fly to their design limits rather than the limits a human can endure.
Drones and unmanned platforms are the future of combat. However they were not widely accepted as such in the 1960s when Star Trek was created which is why they seem to be entirely missing in that fictional universe. And of course, as mentioned before, the storytelling value of automated characters is not as great for entertainment purposes. This does not mean that we can't analyze what Starfleet would be capable of if force to fight for its very survival in an all out war.
This notion of "combat speeds" is not an issue. Imagine a starship "Carrier" that carried 24 drone weapons platforms. They would warp in, drop their shields, release their drones and then either enter the battle themselves or observe at a distance. These drone's themselves are only capable of subspace travel so your starships have the ability to engage warp and leave the battle. However your planets and stationary facilities (Starbases, dockyards, research stations, etc) don't have that ability so they would be destroyed should you not choose to defend them. I build a fleet of 8-12 of these carriers and any required support and scout ships and simply go around destroying your infrastructure. I may never destroy a single one of your warp capable starships (they flee before that happens) but I win the war by destroying everything you leave behind.
This whole discussion is theoretical. Star Fleet Cannon has become as conflicted and incongruent as the bible.
I could quite confidently say that the Federation would easily crush the Dominion in a rematch. In Wrath of Khan the Federation easily destroyed a planet with the Genesis device. Even without the planet building characteristics (which were the desired technological leap that ultimately didn't prove stable) that means I have the technology to destroy entire worlds or solar systems in minutes. Then if you look at STID, transporters can apparently beam objects a great distances (and into starships moving at warp speed). Hell, the Federation could target and destroy every single Dominion Homeworld in less than a day with their Genesis and Transporter technology.
On the otherhand I could state the opposite is true. The Dominion victory over the Federation is assured. Not only does Starfleet seem quite incompetent at times with their tactics and strategy but they obviously don't take defense too seriously. I mean hell, why does Earth, Vulcan, Starfleet HQ etc, always seem undefended??? A pacifist culture like that is never going to win a war against a determined enemy with similar or greater resources.
And I won't even touch the idea that if the Federation had the technology to break down and reassemble objects at the molecular level the Federation has access to unlimited resources because they could transport a pile of manure and rearrange it into a photon torpedo or into a replicant Captain Kirk or whatever other item they needed. This discussion is all for fun anyways.