I fly three Marauders on a regular basis: Paladin,Kronos, and Golem. THE golem is able to change ammo to fit any npc, but missiles take time to arrive and ammo can be wasted4delayed damage. The Paladin has a great tank and if you are being extra frugal can still do good damage with plain crystals (although I use faction/special crystals for rapid completetion). It is also limited to em/therm damage, making it use in certain regions less than ideal. The Kronos remains my workhorse due it’s incredible dps (1450+) and that I can fabricate my own faction ammo quite easily.
While some people recommend the Rattlesnake for mission running, I find it suffers from 2 main problems with the style of how I run my missions. The first problem is that it’s nice dps is based on 2 weapon systems: drones and missiles. This causes an instant damage dealer (sentries) to be combined with a delayed damage source (missiles). You can run either a Gecko or a pair of heavies instead, but the difference of when the damage is applied can still cause a waste of ammo/time. The second problem is the relatively small cargobay of the Rattlesnake. If you are using a Marauder, salvage/looting should be a large part of your mission plan. The Marauder has the 48km tractor beam bonus, you should be using it. Many missions will supply enough loot/salvage to nearly fill the Kronos’ Bay and this adds up quickly. The 'snake just doesn’the have the room to take all your loot and I hate leaving valuables on the field after battle. If blitzing, just get a nicely fit Mach; it is cheaper and clears a room fast.
The bottom line is any Marauder will work fine, base yours on the area you plan to operate/npcs faced. Your ability to manufacture faction/special ammo is also a consideration. Finally, decide if you are going to full clear/loot or just blitz the missions. Marauders are great,but have some serious weaknesses/changes in how you have been running missions. Keep doing your research before you decide and buy! Good luck.