I have an idea, why not adopt a system similar to Galactic Civilizations II about planetary invasions. A kind of land where two factions would fight (as shown below)

This is a good idea. I am sure it would add a lot to the game. All the extra coding and graphics means it will be a long way off though.

Relating this with weapons loadout and ship specialization, maybe something like
#1 using only beam weapons (high precision, lower damage);
#2 a little different, using only torpedoes (high damage, low precision);
#3 using all weapons, for more damage.
There isn't much of a difference between #2 and #3, unless we play around with ranges, and planetary defenses - torpedoes being stand-off type weapons, which you could fire at planets outside the range of planetary defenses, and beam weapons requiring you to close in.

Some interesting ideas here, although the WMD's idea could be a little touchy, so i'd pedantically suggest finding a different name for them. We know the Federation would shy away from using any form of WMD, but EMP's are a nice way of getting around that.

...Incidentally, I had Goldeneye 007 for the Wii for crimbo. It's a good game.

If we go down the route of having unique attack styles like Biological Weaponry, I would suggest having certain random events or consequences from their use. Refugees for instance might spread the disease, or the disease could have a chance of making the system permanently uninhabitable.

Chemical weapons could perhaps have a chance of polluting a planet, transforming it into a Barren planet.

We could even have things like bombarding the system with asteroids if you really wanted to cause carnage. I think there was an alien race in Voyager that used Asteroid bombardment to soften up their enemies.

All cool ideas, but i must say I'm more for the one mike said. As for WMD, they would be extremely effective at killing population, but they should have serious implications when used:

In federation they should lower morale.
They would greatly increase the chance of climate change (maybe even to demon class planet).
Many would do great collateral damage (asteroid bombing, nuclear bombardment,..)
Some races (such as federation) would start hating you.