Those ship engines will eat your economy (both resource and research) dry in comparison with an economy that use more moderately expensive engines overall. Fuel economy is really important for your overall logistical and industrial efficiency. Some over engineered fighter engines with very limited range and fuel cost is nothing in comparison in cost throughout an entire campaign...
Not to mention being easily detected by thermal sensor if you actually use that speed unless you don't make them even more expensive with thermal reduction as well. How much fuel do you put in those things?!?
Also consider you will not be able to cheat fleet training anymore so you will burn ALLOT of fuel and maintenance while doing so. Can it work, perhaps... but for me... I'm too much of an economist for doing that. I rather spend more research into better long term engine technology.
Just also remember that everything ties together, industry, research and military doctrine. Anything very expensive and over engineered must be in limited numbers or you will put brakes on both industry and research which in turn means your quality drops over time against what it should have been. Just take sensors as an example. The larger and more types you research means you put better general sensor tech on hold. At lower tech level a very big active sensors can almost represent en entire tech step advancement as an example. Now when range is not linear you are likely better of with relatively small sensors in general.
I prefer to start building a serious fleet only around mid-game, when I start expanding, so I tend to aim for around 10,000 km/s speed and 40 billion km range for the slowest ships at Magnetic Confinement Era. I don't generally have issues with fuel at that point - sorium harvesters are
really good. Running the entire fleet of a hundred ships at full throttle nonstop for a year will cost me around a million tons of fuel, but at that point, my production is normally in the low hundreds of thousands of tons per year, with a multi-million ton strategic reserve, and a logistical train of tens of tankers and tugboats. I also fail to see why I'd need my ships to cover 400 billion kilometres per year?
And regarding research costs, do note that what you said only holds true for the largest 2,500 ton sensors, which I've never seriously considered. I'm talking about sensors a third of the size; the additional research cost will be offset by the fact that
I don't need to research Small Craft ECM and ECCM, and Fighter Production Rate, all of which are full techs and thus ridiculously expensive. Three 800 ton sensors and their fire controls plus two over-engineered, over-boosted engines will
still not cost significantly more than those three. Here, let me prove it : at around Ion Era [~10,000 RP], the three 800 ton sensors cost 3,360 RP each, their equivalent fire controls cost 840 RP each, a 2,500 ton 1.6x drive costs 4,800 RP, and a 1,500 ton 2.0x drive costs 3,600 RP, for a total of 21,000 RP. In contrast, you'll be spending 2,940 RP on a 100 ton, a 200 ton, and a 300 ton sensor, another 735 RP on their fire controls, 4,000 RP on small craft ECM and ECCM, and 10,000 RP on fighter production rate 16 BP, for a total of 17,675 RP. The difference in research costs is 3,325 RP - pretty much negligible when the next tech level starts at 20,000 RP.
Any way.... remember that passive sensors is what will detect most things. Most passive will detect sensors before they themselves are detected. If you go active sensors you are likely to be detected before you see anything and likely to attract attention and an attack.
It is possible to fire weapons at a point in space after which the weapon can use either active and/or passive to find a target. Since those very small sensors now are much more powerful using such weapons are much more likely and easy to use. You can fire them long before you are detected and just turn around. You don't need an active lock to do any of that.
The point is, detecting the enemy is key... in C# Aurora that means scouting with smaller assets and then protecting them will be important. This is why the fighter/FAC platform will become even more important overall. It will not invalidate larger ships as support for those smaller platform though, they will work good as a combined arms force.
Yes... smaller ships is now more effective at the scouting role which is nice.
Actually, as Steve himself has stated, passive sensors will be better at detecting cooler, nearby objects than hotter, more distant objects. A 500 ton fighter will, at minimum, have one-twentieth the signature of a 10,000 ton cruiser, so thermal sensors will see the ship x4.47 farther out. However, passive sensors have vastly inferior range compared to active sensors, so this is a non-issue. Unless, of course, you're worried about DSTs, but those'll see you half a system out anyway, so why bother?
And that tactic of firing missiles at a waypoint will not work unless the hostile fleet is somehow expected to remain perfectly still and the hostile commander is expected to have absolutely no concept of the military tactic of drunk-walking.