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First of, sometimes, ship will have attached upgrades that tow can't take. By commandering, you can collect it. And sometimes ships has their own upgrade that are permanent, like "decontaminate"/Collector/bomb (Military thing). So if you badly need an upgrade, and you have cleared the ship, this can help.
Secondly, as you said the new ship can hold more. 50+ scrap cap is not necessary, but do not take ships that can hold lower than 30 scrap. Also you can get more ship's slots, which is pretty useful.
Thirdly, you surely have met the "schematic view lost" thing. It occurs when you are using your ship for too long. So taking an new one will prevent that from happening, at best for 5 missions. The first and second point are potionnal, but the third one is what making commandering very important.
Those are the primary differences, but eventually you'll need to swap your ship out. Even if you survive for a while, eventually your ship will start to deteriorate (one of the main symptoms of this is the Schematic view blinking out for short periods of time, gradually getting more frequent) and you'll have to find another.
Salvage and Barge ships tend to have bigger scrap capacity (100+, occasionally), but rarely more than 2 upgrade slots (Salvage is especially bad there). Collector upgrades seem to be more likely on Salvage ships.
Muteki has lower capacity (<40), but more upgrade slots. Even small Muteki (C and D) tend to have 3.
Military ships are very likely to have internal defense turrets and may have the Cannon upgrade - sometimes to the exclusion of other slots. My personal favourite are Military A: They tend to have a scrap capacity between 60 and 80, plus 2-3 upgrade slots (maybe even 4).
Another thing is that you may need a certain ship class to do some objectives.
Oh, I didn't know that. That's useful.
EDIT: Just took the chance, commandering a ship with a 'cannon' and a destroyed 'ship survey' My already installed remote power took the place of the destroyed upgrade. Only 2 slots on both ships.
Cant see the graphic hint for ship type/upgrade options. Would really like some more game info on ship types. How to use the cannon? clicking on it does nothing
My run just ended. Im doing good on drones, 4 (2 in reserve) and upgrades, however am low on offensive upgrades and am now stranded in a system with no propulsion. The only only 2 system I have already cleaned out.
Just like that ...stumped!