Sensor stacking has been repeatedly supported by Brad as someone who loves his sensor boats.  I don't think that removing stacking will be a successful suggestion for redesign.

Also, what you react to as a "frustration", I see as an intriguing challenge.  Effectively, I am defending borders without land troops, as I see it, and that is a very different kind of challenge.  So, I am not convinced how much needs fixing here.

What evidence would you care to provide for the supposed dumbness of a space-warping device's size being unrelated to the size of the object which is using said device to propel itself? You are not talking about a drive system which is accelerating an object according to classical Newtonian physics; indeed, it's entirely possible that to an observer within the region of distorted space generated by the device, the object being moved by the device would not appear to be moving at all. Instead, you are talking about a device which may be distorting space to such a degree that a distance of several lightyears may appear to be a distance which can be traversed in the space of a single week using propulsion systems which cannot exceed c, or which appears to move the destination to the ship rather than the ship to the destination.

I do not disagree with the idea that ship drive systems need to scale with hull size to some degree, but this is for reasons of game balance, not 'realism.' I know of no real reason why a space-warping device that can make a distance of multiple lightyears traversible within a week should necessarily need to be significantly larger on large ships than on small ships.

I have a couple of issues with this suggestion.

Firstly, you're restricting the design space. If I can only put one sensor component on a ship, I either have a sensor component on the ship or I do not; I cannot freely trade between speed, sensor range, and travel range to come up with a balance that I feel is good for whatever purpose the ship is to perform with this limitation. By removing the ability of the designer to trade between these three aspects, you are removing the distinction between an exploration vessel (which wants a balance of speed, range, and sensor range) and an observation vessel (which wants just enough speed to not take excessive amounts of time to get into position, just enough range to go far enough forward to be useful, and as much sensor range as can fit elsewhere).

Secondly, by limiting the attainable sensor ranges without similarly limiting the attainable speeds, you run a great risk of making sensor range virtually worthless. A sensor network that cannot provide at least one turn of warning before an attack hits something valuable is a sensor network whose only value is in the information it provides about the composition (weapons, defenses, hull sizes, number of ships, maybe ship roles) of another empire's fleet (and this information can be obtained by means of scout ships at least as easily as it can be obtained with a much larger sensor network), and your proposal regarding drives will only cut ship speeds by ~50% or so depending on what exactly is meant by increasing the capacity requirement of a drive component by 25% for each increase in hull size. Even with the most generous interpretation of a 25% increase in component size with each increase in hull size (drive components on Huge hulls require 1.25^4 ~= 2.44 times the hull capacity that the same components would require on Tiny hulls), you can still easily fit four or five Stellar Folders onto a Huge hull without severely negatively impacting its performance, as by the time you have access to Huge hulls you can also have a bonus of ~100% to hull capacity (40-50% from specialization techs in the construction branch, about another 50% from a Hyperion Shrinker, perhaps another few 5% bonuses per Helios Ore, and perhaps another 10% per Design Revolution event). 5 Stellar Folders require about 220 capacity at 2.44 times standard size (and this presumes that the player has not obtained any of the drive size reduction specializations on the way), giving the ship a base speed of 31 before modifiers; a Huge hull probably has ~500 capacity by the time you unlock it, and can potentially see its hull capacity increase further.

Thirdly, you are potentially removing a large part of the cost to providing a sensor ship with other capabilities. If the sensor suite does not fill up the hull, there is little reason for me not to provide the sensor vessel with whatever other capabilities I can fit into the hull that I feel are worthwhile; thus, if the sensor suite is sufficiently small, my sensor ships may well be full-fledged battleships without suffering any significant reduction in performance in either role. Even if the sensor suite is large enough to discourage that, I may be able to have high speed, long range, and wide-area sensor coverage all on the same ship whereas under the current model each of these things can only come at a cost to one or both of the others.