Whenever you stage, the command pod should take with it as much RCS fuel as it can carry. So often I jettison a half full tank of RCS fuel only to find my small reentry tank is completely dry.

The fuel transfer option should be available all the time. Not only when docked with something.

-Make all parts resizable. For example, with rovers you may want to make it have a more 'realistic' size, not the size of the largest fuel tank. Or you want a small satellite that only has the size of a fuselage in SR1.
-Fuel lines. If you want to have your engine(s) be separate from your fuel, you can do so.
-small radial engines. These small engines would run on normal rocket fuel, not RCS fuel, And would resemble the small engines on the curiosity mars rover's sky crane.
-backdrop on planet scenery. Though not a huge addition, I still think it would make the planets seem a lot less empty.
-make all docking ports be able to dock with other ports. I always found that having two separate parts for docking was very annoying, so make the docking ports do the job of both the port and plug.
-astronauts. SimpleRockets is so empty without astronauts to save from being stranded on the smoon, without people to die from horrible 'accidental' deaths, without... well, you know what I mean.
-add action groups. It sucks when you deploy your landing legs and you can't put them back up.
-make the RCS engine clusters be able to turn your ship without having to have more than three. If you want to turn your space craft, you can't use the 'up' thruster on one, and your 'down' thruster on the other side. You know what I mean?
-have more command pods. Have some unmanned pods, and manned pods with multiple people that can go EVA with RCS packs on.
-non linear placement system. Make it and so there is a 'snap' option that is like the ship construction on SR1, and a un-snapped option in SR2.

Make it so you can mod in your own fuels that your own engines can burn. Also this site is crowded.

Unless they could be fed with solar panels...

is a cool idea

This would allow bunkering of all necessary supplies for longer journeys.

to the commenter: less than full tanks already weigh less (although there was a bug in some circumstances that didn't reduce their weight when fuel was burnt, but this is now fixed in V1.5)

also, make less than full tanks weigh less.

Being able to have less than 100% capacity of the tanks will be great for 'eco' challenges. I realise this could be tricky to implement, but it would give the game additional real-life flexibility (can short-fill liquid fuel tanks in real life). Maybe this option could be limited to a few individual tanks to make the implementation easier.

'asparagus' really helps in scaling to bigger rockets without creating overpowered tanks and parts - for that build pattern to work we need the ability to draw fuel lines between tanks so that outer tanks feed inner stage motors
http://wiki.kerbalspaceprogram.com/wiki/Tutorial:Asparagus_Staging