I do agree that there is something that feels a bit wonky sometimes in the tonnage/power/fuel consumption equation. But let us approach this systematically by breaking down what common ship types you're going to build:
Military ships (warships):
Not a problem, usually military ship need to be FAST, and size is important. You will almost never want a slow military ship for a variety of reasons (range of engagement, actually catching up enemies, deploying the ships where you need them to be). To be honest, I often use engine multiplier higher than one. Speed is king, and let's not forget that as said before, increasing the shipyard size IS a problem, not to mention retooling times etc. Also, if you need more range you use a fuel transport.
The only issues when you do not want a fast warships are either when you're roleplaying (and then you cannot complain about mechanics, because you're purposefully building a NOT optimized ship), or when speed is not important at ALL. And in those cases you're much better off NOT putting engines on a ship. Just build an immovable weapon/fighter platform, and tug it where you need it with a civilian tug. This has a number of advantages, namely: You can build fuel efficient tugs and so save fuel, the tugs (and thus the speed) can be upgraded without the need of touching the military part of the ship, you have a LOT more space for weapons/ammo/systems, you spend less to build and research the military ships etc.
Military ships (other):
This includes ships that are not warships, but are classified as military ships. Grav surveys, scout/sensor ships, colliers and the like. All these ships needs either a decent speed, or a good speed (if they need to move with/behind the main war fleet). As such if they need to move with the fleet, or move fast for another reason (a fast scout to find enemies) they will have engines similar to a warship, and so with a high multiplier. If they don't, then I usually stick to 50% commercial engines to save fuel and have a good range while still having an acceptable speed. Even before ion engine tech, this is usually good enough range/speed for grav surveys and the like, because you generally scout ahead of time and such.
Civilian ships:
The only general thing is that you need to have the necessary range for your mission. So, at very low tech levels this might mean you change something in order to gain more range. But even just from ion engine, this is no longer a problem usually. Let's see case by case.
Tugs: one of my favorite ship designs. Tugs generally are 90% engine, 10% fuel space or something, so nothing wrong with the current model. Just build the most fuel efficient engine you can, and add as many as you need to obtain your ideal tug. No other considerations are required, you generally do not care how long it takes to move the tugged ship. If for some reason you need a fast tug instead, just make a tug with all 50% commercial engines on it, and you're done.
Terraformers, sorium harvesters, gate builders: if you're putting engines on these ships, you are doing it wrong. These ships needs to move rarely. Actually, terraformers and sorium harvesters need to move once every few years at most. You do not want to put engines on these. In order to put engines on these ships you need to increase their size immensely, which in turn means more cost, more fuel used/immobilized, bigger shipyard needed etc. Just build them as immobile, engine-less platforms. Cheap, faster to build. Apply tugs as needed to move them around
Cargo ships and colony ships: if you're doing it right, you will need FEW of these. And often, 0 colony ships alltogether. Unless you purposefully killed the civilian sector, what's the point? The civilians can and will move all of these for you at basically no costs. You may need a few, in order to move minerals or installations at critical times. In that case speed is generally important, so you stick to 50% commercial engines anyway
Geological survey ships, team transport ships: speed generally matters, so use 50% commercial engines. If it does not (example, far away system you want to geosurvey for the next decade expansion plan), then you use the most fuel efficient engine you can build. Let me point out in these cases I'd never add more engines to "optimize costs etc" as the opener posted. Why would I? If I do not plan to move into a system for at LEAST 10 year, it makes no difference to me if I take one or three years to survey it. Oh and about the team transport ships.... You use them right? You're not "cheaters" that magically teleport teams around, right?
That covers the most common ships types I think. So after looking this through, I'd say that the current system, while not perfect, is not problematic because you generally do not want to optimize fuel cost/speed by adding more engines and thus increasing size. Of course, if you do not like to use tugs/weapon platforms, or if you do not like to use civilian shipping lines for your needs, then it becomes more problematic. But in those cases you're not really "optimizing" the game anyway, so I do not see the problem there...