1) In stock, they cost more...
In my mod (see the mods thread), they have more hitpoints, and do more of what they do. Lifesupport level 6 has 50% more life support capacity than level 1, for example, so you could replace the 3 life support required by a battleship with only 2 level 6 components.
Crew quarters provide more crew, and hence more repair rate, etc.
2) The storms are quite hard to see through, and although you can target through them, I have a very low success rate at randomly clicking in there to find a planet or ship I know is behind it.
Once we get more abilities for the storms, they'll be more exicitng
3) You can place your scanners in any slot they're allowed to be in.
For a mod, you could distinguish between inner and outer hull slots by making a new slot type, and forcing things like scanners to only be in outer hull slots.
4) Yes, however in stock, there may be a limit of one per ship.
5) The tonnage of the ship is the major difference between the MK1 and 3, and that is listed under the "ship statistics" tab in the inventory window.
6) That would be nice.
As an immediate measure, you could separate the cargo jobs into "Courier" and "Shipping" missions.
Make the description of each indicate such, and then tweak the max/min # of cargo items to match.