Nick -
The situation you describe makes perfect sense to me. Briefly, your room's too big for the SL-3's. But please read my explanation as to why this is so, because it isn't obvious at first glance.
The woofers on your Martin Logans approximate a point source, while the panels approximate a line source. And sound propagates differently from the two - under anechoic conditions, sound pressure level falls off by 6 dB for each doubling of distance from a point source, but by only 3 dB for each doubling of distance from a line source. If we match the levels of a true point source and true line source speaker at 1 meter, then measure again at 10 meters distance, the point source speaker will have fallen off by 20 dB but the line source speaker by only 10 dB!
In a real-world room, the reverberant field fills things in somewhat, and the panels aren't tall enough to truly approximate a line source. But I took some measurements in my living room once, using a pair of hybrids (SoundLab Dynastats), and the results were rather interesting:
With a pink noise source, at one meter the woofer was 1 dB louder than the panel; at 3 meters (normal listening distance) the levels were exactly the same; and back at 8 meters (the practical limit in my room) the panel was 4 dB louder than the woofer. So as you can see, the perceived tonal balance will change with listening distance.
The tonal balance also depends on room size, as a larger and/or more acoustically porous room (lots of hallways or doorways) would have given an even greater discrepancy between woofer and panel because the reverberant field would provide less fill-in in the bass region.
So I hope you can see that a hybrid electrostat is even more of a juggling act that it appears at first glance - the relative levels of woofer and panel have to match up for your general room size and listening distance. Some hybrid electrostat manufacturers build a great deal of level adjustability into the speaker, and some build a wide range of models so that you can match the right size model to your room. Martin Logan falls into the latter category.
If you read a lot of consumer comments on Maggies and Martin Logans, you'll find that comments on the tonal balnce of the Maggies are fairly consistent, whereas comments on the tonal balance of the Martins vary much more - one person says they are too bass-heavy, another that they're thin and anemic, and yet another that they're just right. I strongly suspect that the variation in perceived tonal balance of the Martins has more to do with how that particular room interacts with their combination of line source and point source propagation than anything else.
As I recall the crossover on the SL3 is in the 300 Hz ballpark, so adding a subwoofer would still leave a hole in the midbass and lower midrange. But it would still improve the overall tonal balance. My suggestion would be to add two small subs - one for each channel - so you can run them up fairly high without spoiling the imaging. Look for a sub that is smooth and sounds good up into the midbass region, and that can be crossed over fairly high, rather than putting maximum emphasis on bottom-octave extension. What you'd like to do is add a pair of level-adjustable woofers to augment the ones in the SL3's, rather than adding a deep-bass-only subwoofer. I would imagine there are some rather inexpensive subs that would fit this description, though I don't know of any offhand.
Best of luck to you,
Duke