An idea I've entertained for quite some time now is the idea of boarding parties. I admit, this isn't an original idea of mine. I picked it up somewhere in the forums back in Open Beta when the idea of PvE first came on the table.

The idea runs something like this.
In EvE, there's a battle about to take place between two groups. Both groups put out a DUST call for Mercs to help them in the coming battle. During the battle, select ships carry a group of Mercs near the enemy fleet and launch a boarding vessel. The vessel can be shot down before boarding. Once boarded, the mercs then have to fight thier way through the decks of the ship to get to the bridge. On the bridge they disable the ship and initiate a self-destruct sequence which causes the ship to go boom, and one less ship to take care of for the EvE fleet outside. Of course, there's every possibility the ship blows up before the mercs reach the bridge.

To counter the boarding parties. EvE pilots can invest in two different things. They can either
A) Keep the hired mercs onboard to counter other mercs, giving the ground pounders some PvP action.
B) Invest in boarding defence gear located inside the ship to ward off intruders.

Either of these methods will increase the time it takes for the boarding party to make it to the bridge as there would be doors to hack open, enemies to fight (NPC or other Mercs), and even automated turrets to destroy.

Naturally, we couldn't board some of the smaller crafts, and the larger ones would naturally be harder to board at a base level due to the sheer size of it and the time it would take to simply clear the decks.

To add to these ideas. Here's another one to try on.

We all (or most of us at any rate) know about Wormhole Space in EvE. It would make for an interesting Salvage-type mission to have an EvE pilot explore Wormhole Space with a team of Mercs to pick up the smaller bits.

If you'll recall the ''Immortal'' video signaling the start of the DUST Mercenaries. The discovery of our implants was made by an extraction team who got off a ship and explored the Jovian Ruins on foot. I dunno about you guys ... but I want to be the one who discovers the next major advancement in implant technology created by the Jove.

So at a basic level. While the EvE pilots do thier thing in WH Space (I don't actually know how it works myself ... I've yet to play EvE sadly). And at the same time, they drop off the DUST Mercs on a large, ruined structure, to find what they can and add it to the salvage.