The spore ships in DA are a nice thing I like to use, but it could be more challenging. For example, you could have a basic spore tech with a 10% chance of success, you could keep researching and improve their terrible chances of invasion.
They also shouldn't be able to invade enviroment worlds without the proper techs IMO. Think about it, In a world of radiation, those spores would be killed instantly. They would just not work on these planets unless you made superspores, which just sounds really cool to use. I also have fancied the idea of having crystal ships, like tiberium, that would have different chances of success and time to assimilate that planet, which would create a radioactive planet, neat huh? Read the next paragraph to know what the heck I'm talking about.
The spore ships (and maybe crystal ships) should work slowly to kill that enemy. The enemy, of course, would have a chance to contain the outbreak. You would see tiles being creeped upon every turn as it infects their planet and their population plummets. (esp if the spores get a farm.) They could dispatch agent-like units to hold back and possibly contain the spores from spreading. They would have to employ walls of these agents to make sure it doesn't get through or else the planet would fall much to easily. They could also be on a tiberium planet so stave off the spore infection, or vise versa(if they are desperate enough, they could turn their own planet into a tiberium world). They could also research technologies to put a crutch in the enemies rate/chance of infection. Knock that 50% chance rate down to 20%. These ideas the defenders a sporting chance to protect their planet without instant and total annihilation from a couple of spores.
On another note, I think it would be neat to have a crystal line of weapons. Have something like needlers from halo, except on a massive scale. I could just imagine a needler shooting at a ship with lightning speed. Shreading into the hull and exploding a few seconds later for even more carnage.

(I always wanted a tiberium needler
Tiberium Needler )
I'm pretty sure kryo and many other people will see this, so feel free to give me your ideas and feed back.