Commander and Ship speed

You can upgrade (with the right tech) the commander to an  Admiral (and other stuff like a privateer).   However you lose the Commander bonuses for other stuff like defensive upgrades  (cant remember exactly what off the top of my head).

I personally think the added moves and logistics points of the Commander is worth more than the upgrade to Admiral is.

I would however like to see the Commanders ship have some of it's own firepower.  

You cannot custom design the various Commander ships... so for example, you cannot upgrade the Commander Ship to have superior engines. It currently utilizes 2 HyperDrive Plus engines (so does the admiral ship).

Any way to mod them to be slightly faster?

Absolutely . I'm working on stuff like that right now.

You can do it in two ways... 

1) find Commanderblueprintsdefs.xml

.... Find the line that says hyperdrive plus.... Change it to warpdrive or just copy the whole line a few times.

2) find the commandercomponentsdefs.xml and add a speed boost ability to the admiral and Commander ship components.

Option 1 is much simpler and easier in my opinion. 

@Gauntlet

Do you know a way to add a ship class without having to copy the whole shipclassdefs.xml to your mod folder.

I have a Commander upgrade option that upgrades the commander ship to a faster ship if you have researched the required drive tech. 

Seemingly you can't do this... I've recently tried to do much the same, but the game seems to hate append style files for the shipclass.  

But yeah... In theory, just a renamed file copy of shipclassdefs and remove the erroneous days.

But I don't think it'll work.