The first thing is the role of bass in the overall musical picture. All recorded natural sounds and complex generated tones have both a fundamental frequency and harmonics / overtones. The fundamental frequency is always the lowest and the harmonics happen at the same time as the fundamental but are higher in the frequency spectrum. There are both even and odd order harmonics so, without getting into too much detail, there is a multiplier (called the ’order’) that determines the harmonic.
For example, a 2nd order harmonic is the fundamental multiplied by 2. So a 2nd order harmonic of a 1,000 Hz fundamental is 2,000 Hz and the 3rd order is 3,000 Hz. As you can see, depending on the fundamental frequency, higher order harmonics in the midrange can affect the treble quite noticeably.
With the lower frequency values of a bass fundamental, you can see how many orders of harmonics still fall within the bass range. 30, 40 & 50 Hz are essential fundamentals in the bass range and have 2nd and 3rd order harmonics in the bass range as well. 30 Hz will have 60 Hz and 90 Hz harmonics.
For a tone to sound natural (and for it to be heard as it was intended to be heard in the mix) those tones must be in the proper balance. This doesn’t mean they all have the same apparent loudness, as most acoustic instruments and voices have a loud fundamental and decreasingly quieter overtones. If an overtone is louder than its fundamental, the note or sound appears distorted or unnatural.
Several essential problems arise from trying to reproduce bass fundamentals in a playback system.
1. The speaker itself. Most speakers are compromise designs in the bass range. Truly fluid, natural sounding bass requires a speaker enclosure with a large internal volume. This is at odds with many listeners who don’t want giant speakers dominating a room, so we wind up with things like bookshelf speakers and other speakers with rolled off bass. Many speakers begin to roll off their bass response starting at 60, 80 or even 100+ Hz. This means that, irrespective of room dynamics, the speaker itself is incapable of portraying any sounds with a fundamental frequency below the roll off point in the way they were intended to be heard in the mix. Their overtones are perceivably louder than the fundamental. So the first rule of truly natural bass is a large speaker that can go LOW and has a flat response throughout the 30/40/50 Hz region.
2. Using a subwoofer as a fill. Subwoofers can be used to fill in the fundamental frequencies that are deficient in the primary loudspeaker’s design. However, they must be tuned with extreme care and precision to the frequency response of the primary speaker(s) they are filling in. This is often referred to as "blending-in" the subwoofer. The first thing required is an accurate understanding of where the primary speaker begins to roll off its loudness output in the bass range. Any decent subwoofer has both a level control and a variable cut-off frequency in its crossover circuit. You use the primary speaker’s roll off frequency to set the frequency cut off in the subwoofer’s crossover circuit. By setting a cut-off in the sub, you prevent it from playing and therefore reinforcing higher order harmonics that the primary speaker is capable of producing, which would, again make them unnaturally loud. Next you have to adjust the loudness of the subwoofer to ensure that the fundamental frequencies it does reproduce match those of the primary speaker. So, if you play a series of sine or warble tones without harmonic frequencies like 30/40/50/etc up through the cut off frequency into say the 125 and 250 Hz range, the tones played by the subwoofer should match those of the speaker. (Measuring a speaker is an entire science in itself, but to prevent room interactions these measurements I describe should be performed at the speakers, not the listening position.)
3. Using the right subwoofer as a fill. Another problem with using subwoofers are (often inexpensive) theater subwoofers that are really only designed to operate in the LFE (low freq/subwoofer) channel of a home theater. These subwoofers are designed to kick like a mule to give you the concussive beats of a T-Rex's footsteps but they don't necessarily care about reproducing all bass frequencies evenly. A musical subwoofer has much more care put into its design (presumably) and attempts to control distortion and driver ringing in a way that presents bass evenly across its usable frequency spectrum.
4. The Room. Once the playback speakers are in balance, you have to consider the room. Bass is extraordinarily more difficult to control than other frequencies. Bass is omnidirectional, so it likes to go everywhere. Like circular ripples from a large stone dropped in a still pond, the circles travel outward, slap the sides and return as more ripples. Where the reflected ripples interact with the primary outgoing ripples, they make the height of the waveform, its apparent loudness, go up or down. In a room we see this as reflections off the floor, ceiling and all walls interacting to make an interference pattern of hot and dead spots. What’s worse, the pattern of hot and dead spots is unpredictable in practice because, although the room and the speaker positions are fixed, the reflections interact differently at each wavelength (frequency) of sound. So the pattern of hot/dead spots at 30 Hz are different than those at 40 or 50. The only way to bring all this under control is through absorption. If your floor is concrete, you can’t treat it. Bass traps in the corners can help a little but it’s surprising how much deadening mass that takes, and it is mass only that absorbs bass energy. It takes to make an appreciable dent in the amount of bass actually absorbed before you begin to fix these problems. In a world class recording/mixing studio, for example, they might build with 12-inch deep studs and fill the wall cavities with carbon pellets just to control bass. Most listeners can’t commit to this level of architectural intervention and instead do best effort with speaker/sub placement to minimize their bass reflections, then tune it with DSP until they can live with it at the listening position. DSP is a band-aid for lumpy bass. You just cannot solve interference at all positions in a room through equalization.
Even if you only have a standard stud depth in your room, filling hollow wall cavities behind dry wall is essential. Sound is energy, it is in a sense, heat, and absolutely stuffing your walls densely with fiberglass, rock wool, recycled denim, or another insulator will reduce the air in those cavities resonating. This is because deep bass not only bounces, it also loves to resonate other objects. Standard drywall on studs, especially with a hollow wall cavity, just LOVES to sympathetically resonate with bass like a huge wall sized speaker driver.
In summary, many systems can’t produce natural sounding bass and many listening environments reinforce bass producing unnatural and uneven distortion. The problem here is that bass is complicated in its presentation and difficult for non-experts to articulate how it is deficient. They don’t know what’s wrong, they just know something is unsatisfying. If you don’t know what’s wrong with bass, you can’t fix it with something like DSP/EQ without causing more problems than you solve. The best advice I can give when evaluating bass is that more is often not better, but not enough is just as bad. If your sub is obviously present, it’s probably out of balance. It should blend seamlessly and gracefully into the entire musical picture.