Motivation
I don't like the controls of the old vertical scrollers, because sometimes it is very difficult to understand which keys are used for which weapons/weapon change/systems.
On the other side I do not like the the idea that one hand is controlling the space ship (arrow-keys or w-a-s-d-keys) and the other hand is just pushing the shoot key.
Idea
To come around this problem, I thought about a WoW-style (World of Warcraft) control (related to the fps games genre):
one hand is on the w-a-s-d-keys (as usual for fps games) and controls the movement of the spaceship completely. The other hand is on the mouse, left mouse button (LMB) would be the fire button (nothing different, but the LMB is used to fire).
Additionally:
With the mouse, the player can control an in-game menu on the screen to select different weapon systems, select different weapon modes and perhaps do also the system energy balancing.
This could look like the WoW GUI:

Focus on points 22, 8 (the points on the bottom of the image).
At this point I want to apologise for using pictures of WoW to illustrate Orxonox gaming topics, but Blizzard does (as they always do) have a very good understanding about how a GUI must look like to be comfortable.
This GUI would also bring some additional benefits: it would make the game much simpler, therefore making it more playable for a bigger audience.
One could also think about using the mouse movement to look around the spaceship a bit (looking backwards, forwards, etc) the view will always automaticaly return to the normal vertical scroller state. This would also enable the player to look at the ship closely and from different directions (what someone would probably like, if he/she upgrades a ship with cool weapons

What do you think about it?