Well, I've weighed in on jump shock, so here goes for the rest.
On the Transit Drive
--- The fuel thing is definitely the lynchpin to this suggestion. As given 1HS per fuel unit IS VERY, VERY broken. The idea was that ships might carry... 1~3... 5 units of fuel, tops? The whole idea was that this was to be a very limited resource. The concept that fuel storage got more expensive as it got more efficient was meant to reinforce that this was very powerful. The idea of a Transit Drive with 0 fuel built in was so that small ships could have a self jump drive for much less tonnage than a full on jump drive. The numbers would need to be tweaked... a lot, but the idea is that realistically speaking, a ship is not going over 3 Transit Jumps without being either absurdly expensive or cutting into mission tonnage, while a ships is NOT going over about 5 Transit Jumps without being absurdly expensive AND cutting significantly into mission tonnage.
The counterarguements that I agree with is that it doesn't matter how expensive it is, or that a ship that can do it 3+ times can't do anything else... it's that a ship that can do this 1 time is broken, as it has an ability that can easily counter an entire combat doctrine. As for a 0 fuel version to reduce tonnage compared to self jump drives, I'm also against that as it deprecates the utility of the jump drive efficiency tech line. By that I mean that with enough research, you can already make a 1hs jump engine that can jump any sized fighter.
That being said, I see the desire and utility for a way of transiting to distant secondary stars that don't already have stabilized lagrange points. The only way to reconsile this with my concern is for the transit drive to have a spin-up time: essentially the order to transit would also create an order delay before the transit. Which also happens to be one of the proposed mechanics many, many others have proposed for improving jump point transits. If that's doable (and it should be since the game can insert orders on more complicated criteria like auto-including lagrange points), then that's the only way I'm seeing of getting behind the transit drive.
On Pulse Sensors:
As things stand in the game now, we really aren't seeing continuous movement of objects. Actives show us where things are right now, and the game can also show us a movement trail extrapolated from the last snapshot. If someone wants to rp that sensors are providing a continuous feed of data or rp that sensors ping every 5 seconds, both fit with the current limits of the game. If someone really, really wants to rp that sensors ping less often... they can turn their actives on and off.
So, I really don't see the need for a new system. Even if it's implemented in a way that's well-balanced against existing active sensors, a big chunk of the players aren't going to use it or appreciate that it's there. At best it's a QoL improvement for the players who want to automate slower sensor pinging. At worst it's adding design choices for everyone including those who would rather keep things as they are now.
On Commercial Engines:
I'm in favor of changes that allow for smaller commercial engines. I don't dislike xeno's suggestion, but I don't know if it's the best way to facilitate that goal. Likewise with serger's suggestions. I see the appeal of a ramscoop (or whatever other explanation is used for fuelless commercial engines) to reduce player/AI special rule cases. The caveats there is that it reduces design choices (but I really don't know how large a % of the players enjoy balancing speed/fuel usage on their freighters) and there would need to be a check to prevent commercial engines on military craft (as I don't see it as desirable to allow fuelless engines on warships, no matter how slow they are; at that point you might as well get rid of fuel altogether). Granted, that second point is mitigated in that with seperate tech lines, an engine wouldn't be designated as commercial just because it's big and slow, and the game can already check for similar ship design rules. I also don't know if an additional tech line(s) are desirable for the overall goal (smaller commercial). Looking at how jump engines are handled, similar things can be done that way: toggle the design project to commercial, and it would alter other features (power per HS, max boost, etc).
I see the crew requirements as the need not only for manpower, but also the various food stuffs, etc. The "Life Support" as it were. Also, I feel as though the comparisons to wet water ships are relatively poor. In space, it is far and above more difficult to maintain things. Whether Real Space or the Aether, starships of any stripe are very likely to be significantly more difficult to maintain and need significantly more supplies to keep those crew members alive.
That said I STILL maintain that I'd really, really like to see Jump Shock prevent a ship from Jumping while under the effects of it.