E strings, as posted above, need care and feeding when installing. Check the bridge saddle to make sure it has a good burnished witness point, and the same with the nut, that it is wide enough and slopes slightly back from the witness point. Then at pitch, slightly stretch it, re-tune, press down a little bit on the bridge saddle and nut slot to seat the string core. Make sure there are even wraps that don't go down too far on a Fender-style headstock, just a little more angle than the A string or the angle of the D and G strings from nut to string retainer is sufficient. Use strings that only the leader goes around the tuner post, or at most only a partial wind of the main speaking length of the string, for ease of tuning.
Check the tuner bushings, the neck screws and plate, the bridge screws and plate, the intonation screw, etc., all for moderate tightness so as little resonance as possible is being sapped out of the string into the body. You might have to trim the intonation spring so it doesn't bind as you adjust intonation. Yes, even that can kill sustain.
My hand perspiration eats nickel, so I used to have to purchase extra E strings when purchasing sets, even with something with more iron than nickel in the mix, like Progressives. Even my favorite Fender Flats E-string, being wound with ribbon stainless steel, went thumpy before the rest of the set and I had to get an Ernie Ball E string because Fender doesn't sell singles. I still keep extra E strings in the case, and the next-oldest set that just came off the bass, in case of breakage or complete death of tone, so I can keep going at a gig. In the middle of a song, Boom-Boom-Boom-Thud is a lot less noticeable than Boom-Boom-Boom-Twang from a new string.
Sometimes, it's just the nature of the beast. The reason the E string has a more hollow tone coming up the neck is that the larger core is not as flexible as the other strings, so it doesn't want to vibrate in partials as easily; the relative presence or absence of upper partials is what we perceive as bright or dark in tone.
Another equalizing factor is that I change my passive tone cap from .047 to .033 to retain more mids. I can turn down the tone from about 10 to 7 or 8; this cuts the twang off the G string but leaves as much tone intact as possible from the lower strings, including especially the E string.