Been rocking the 99 Noirs for 2 days now. To my hearing the pads make a huge difference.
Similarly to the measurement plots on Massdrop, and Tyll's observations the pads that come pre-installed (the latest gen "Stock 99" large hole ones that come with the Classics and Neo) recess the mids and some highs a little too much, particularly 3.5-5 kHz and 8kHz. Sound becomes a little v-shaped and the highs - slightly peaky, but still not fatiguing. They do make the sound stage a little wider but some tracks sound like my head is in a cadboard box. On the positive side because of the stiffer foam my ears barely touch the cups and feel airy.
The "new original" pads (the small soft ones with the foam filters) sound a lot more balanced. I haven't heard any of the Classics versions but I think that's the signature everyone originally fell in love with. Because of the soft foam my ears touch the drivers and they feel a little stuffy. Won't be fun to wear them on a hot day. Anyhow, I do hope Meze releases these to be purchased separately, or ideally create a new revision that has the shape of the stocks but creates this sound sig.
Btw I believe MD has the pad dimensions erroneously switched. My "stocks" measure 104x85x24/67x50 mm while the "new originals" measure 96x85x25/60x50 mm.
EDIT: I want to add a big YMMV of course. Some folks don't hear much of a difference between the pads, and nothing on mine has been broken in yet - pads or drivers (if that's even a thing).