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.

This has been discussed briefly a couple of times, and I've generally rejected it because of the extra work involved, and because the ground-based combat is something of a 'secondary' aspect of the game. Instead, I was planning on something similar to MoO 3 with different targeting modes:

• A targeting mode which favors accuracy and minimizes collateral damage at the expense of total damage inflicted (lowest negative morale impact).
• A balanced targeting mode (medium morale impact).
• A 'total destruction' targeting mode which maximizes carnage without regard for collateral damage (significant negative morale impact).

The combat would occur in phases, tentatively with up to five phases allowed per turn. During each phase, the player could (un)assign ships to the assault/invasion effort and adjust tactics. Alternatively, if the player is not interested in an invasion and simply wants to erradicate the population, there will be an option to unleash total ordinance for massive damage all at once (in a single action instead of phases).

I might consider bringing different types of WMDs (weapons of mass destruction) into the game, which could be interesting if they varied by race. For example, the Federation might use EMP-style devices (damaging infrastructure without harming the population) but they would would not be able to use biological or chemical weapons. The Cardassians and Dominion would probably use anything.

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.

The episode 7x23 with the Talaxians!! (VOY: "Homestead")

The Romulans use the thalaron radiation
The Dominion use the Houdini mines

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.