This achievement is a massive grind, and there is no shortcut around it. You have to kill 1000 of every enemy type, including the exceedingly rare ones. You will only need to focus on the Hunters, Hydras and Scarabs for this achievement, since getting 1000 Scarab kills means you will kill above 1000 of everything else guaranteed.
You can see how many kills you have by pausing, going to Help & Options and then Game Statistics. This section will tell you what each enemy's name is too, so you can follow this guide more easily.
Here is the general strategy to employ:
* Use the unlockable Overkill mode. Spam bombs whenever you get close to dying.
* Play until you reach waves that contain the enemies you need to kill. You can, of course, know when one is coming up based on what giant enemies are lying dormant in the background. If you see a big Scarab, stick around and wait for it to come alive.
* When you reach the correct wave, head out into empty space somewhere and go in circles to spawn new Scarabs. This is to avoid killing the octopi, so you can stay on a Scarab wave for as long as possible. You can keep grinding Scarabs even after the Hunters start coming out.
* Keep in mind that Scarabs and Hydras usually spawn "in pairs." Meaning after a Scarab wave usually comes a Hydra wave and so on. Hydras are less rare, though, and you will need to focus almost exclusively on Scarabs.
You will want to milk Scarabs as often and for as long as possible. Every time you hit a Scarab wave, use the above strategy to stay in it as long as possible.
There are a few variations you can use to make this more efficient:
* You can set aside 2-3 hours for each session and thus head further into the game to make Scarabs spawn more often. This can be really boring, but Scarabs generally don't start showing up in big numbers until later in the game, so it is the most efficient strategy. I recommend watching a movie or an episode of a show or something as you do this!
* Play only 15-20 minutes into Overkill mode to reach the first Scarab wave, then quit out. This will net you fewer Scarabs, Hydras and Hunters overall, though, and will take longer overall, but is less boring and you can play in 15 minute sessions rather than 2 hour ones. Up to you!
* You can either try going for Hunters when you're farming Scarabs - you will inavoidably kill many Hunters whenever you milk a Scarab stage and stay on it for too long - or you can leave Hunters alone until you've secured 1000 Scarab kills. I used this strategy and I had about 500 Hunter kills after getting 1000 Scarab kills but the Hunters come so often and in such aggressive numbers that you can reach 500 kills in about 45 minutes when you focus solely on them.
Unfortunately, you cannot use a turbo controller to let the game play for you. If you rubberband the bomb button, you will find that enemies simply stop spawning immediately. This achievement has to be done manually and it WILL take a long time. My achievement popped at around 30 hours played and I don't think completing anything else in the game took longer than 10 hours.
Hopefully this guide makes some sense and helps at least some of you cut down on the grinding time this game demands. There really isn't a deep strategy to it - just head for Scarabs and farm until you're forced to switch levels - but I've tried to make the solution as detailed as possible since this is an incredibly dull achievement. Good luck and hope you find some way to kill the boredom while attempting this!