Some of the difference you hear could be height adjustment. The closer the pickups are to the strings, the greater affect smaller adjustments have on individual note timbre. At typical 2~4mm heights, I find a ~1/4 screw turn can make a significant difference in fundamental harmonic note strength, which essentially affects the “bass” response up to the highest note on the guitar (~600Hz), and includes the 2nd and 3rd harmonic of each note to some extent. The Microcoils may technically have stronger fundamentals than the Keystones, but the higher inductance of the Strat Keystones increases the midrange balance with the same pot values. It likely includes some of the upper-bass range, but the Microcoils should still have relatively stronger fundamentals. I'm not sure of the magnets in the Keystones. They may be a bit stronger. That of course affects signal strength and limits how close the coil can be to the strings before the magnetic pull audibly affects the notes, both factors depending on the string material – pure Nickel being weaker than Steels or Ni/Fe alloys.

The other factor could be your cable capacitance. It's a significant part of the tone. Even with 250k pots, a fairly high capacitance cable could easily put the resonance of the 1.4H AlNiCo Microcoils in the 4~6kHz “presence” range, making them pretty bright, while a lower C cable would place the resonance above the typical guitar speaker range, making them more even sounding with a nice “airy” high end. Even an average ~400pF 12' store brand cable should be fine. The Keystones would probably sound pretty bright as well with the same high C cable though, so it's probably the affect of the relative midrange increase of the higher inductance Keystones, and possibly the height adjustments.

A low C cable can produce a less brittle high end from the AlNiCo Microcoils, as the resonance peak will be above the “glassy” presence range and less emphasized – producing more of a sweet sparkle overdriving the preamp stage. It's also generally recommended to reduce the amp Treble, boost the Midrange, and engage the Bright switch and/or increase amp Presence for sweet extended highs. Reducing the Bass can improve clarity, but it also affects amp overdrive sustain, so it's a trade off. Try all these things together and see what you think.

BL Equipped Guitars:
-Parker NiteFly V1 Strat type: Wilde L280SN/L200SM/L200SL/L280SL w/L-filter & MT.
-Agile ST-625EB: Wilde Microcoil S set.
gckellochguitartech