They are both 1x3x1 L T2 / Jet S force 380 / 300 Mass 842 / 743 Heat 773 / 450 Rads 12 / ?? On paper, the Large T2 seems to be better but they are a bit heavy.
A simple way to solve this is by dividing the Force by the Mass, and compare results : the higher result is the "better" one. For example, you can already intuitively guess what engine will perform better when trying to move the same mass (because you have to take its own mass into account+ the vehicle's mass): Engine A : Force = 100 and Mass = 10 ---> 100/10 = 10 Engine B : Force = 200 and Mass = 10 ---> 200/10 = 20 Once this is understood, simply apply the same method with any thruster. Here for example the thruster L T2 has a ratio (result) of 0,45 and the Jet S has a ratio (result) of 0,40 - which one is more efficient ? Then you can compare power usage and CPU, but for strict "Force" this is a simple method for comparison.
Indeed. Not that it's super-useful, as the boost typically equates to something like an extra 3-5 m/s. If you're really, really adept, you can use it to evade some incoming fire from things like Zirax POI's, but I wouldn't count on it. IMO, the Boost should be increased between 2.5 and 3.5 times what it is now, possibly more for the largest of jets.
I've found the boost function gets a heck of a lot more use now that space is so much more dangerous. It's great for getting away from angry drones in a hurry. I wouldn't bother with jet thrusters for maneuvering, but they're a good choice for your forward thrust vector in spacefaring SVs, both armed and unarmed.
I don't think there is no one answer fits all for this. There is the total mass of the ship (including whatever engines are fitted) and the total thrust generated - which combination fits you needs better? Then for jets, there is a speed boost (which TBH is so tiny in its current form as to be barely worth mentioning - as @IndigoWyrd says - its needs a huge boost to be sufficiently useful given its short duration as well). You probably wont use smaller jets for directional thrusters - maybe just rear facing. Of course with a bigger SV, then you will probably be using jets for front, back and up just to get the thrust needed without requiring silly numbers of thrusters. Sometimes one or the other may be a better cosmetic fit regardless of use/need. M2 and L2 are heavy for the amount of thrust they yield, but that extra thrust gets more useful on heavier ships that are relatively less impacted by the additional mass of the thruster - ie where the relative increase in thrust is more than the relative increase in mass and you do really need the extra thrust and are less concerned about any other directional maneuverability loss from the extra mass. Best go into creative and load the vessel you want to fiddle with and try different combinations, look at the stats panel and get a feel for what you like to go with the vessels purpose and a flying style your are comfortable with for it in it intended environments (planet vs space and gravity). Sometimes you may need to adjust flying style as well to suit the craft and it thrust placement. I have found on some ship designs using M2 and especially the L2 variants that removing several of them can make a big difference to overall ship agility without sacrificing too much essential lift and back thrust - it can be quite a fiddly trade off that varies from one vessel to that next.
For most of my SVs I use the Jet M. Compared to the normal M and L they're in a completely different ball park, with the "normal" thrusters having a ratio of 0.6 and the Jet M having one of 1.6. That is for pure "building" fun not taking energy or cpu into account. The Jet XL has a ratio of 3.6... it's insane, and it's big so making relatively "compact" builds with this is quite a challenge. They offer lots of surface for their hit points pool (4500) but if only the end of the thruster is exposed their HP per face (3x3 ) is 500, which is not too bad. This is meaningless, as the whole 4500 HP have to be drained to destroy it, but it's just a figure to compare HP-per-exposed block.
I've used the XL Jets on a few builds - my Planetary Lifter (now somewhat defunct, as SV's can mount mining lasers) used 4 of these - two for upward thrust, two for forward thrust. I've also used them for my Saturn V tribute, but by and large, they are rather challenging to use due to their size, fuel consumption and power requirements.