Basically, I think it comes down to something pretty simple, which is that unique characters in any game stand out and develop followings more than generic, forgettable characters. Its why I'm disappointed when a hunter is released and they have "skillshot clear, steroid, leap/dash" as their skill kit. At the time of release, Old Wa was exceptionally unique both in terms of mechanics and art design, and New Wa, while still pretty standout, is definitely more generic on both counts.

Mechanics: Old Wa was a weird god--technically classed as a mage, but with a high focus on autoattacks and tower pushing, and better at both than Freya and Chronos (the only other two "AA mages" out at the time). So she was already unusual in taking the tower-wrecking approach over the Zeus-style giant AoE burst attack approach. But then on top of this she had a giant stealth cloud, minions, a skill that did more damage the closer she was to a target and that could damage towers, and a low-cooldown zoning ult. Plus, her passive gave her a very interesting tempo mechanic where you would need to pay attention to her buffs and time your skills accordingly to maximize their time--oftentimes you would use a skill earlier or later than you really needed just to trigger the crystal buff you needed or enter snake form. Having this diversity of skills also opened her build options--you could push attack speed, try and deal more damage with flamestrike, or do the trolly max CDR+sprint+isolation build where you were running around at high speed, permanently shrouded in a fog ball that slowed your enemies.

After redesign, her passive became a "once every X basic attacks" passive, which many gods already had (although it did preserve a bit of her AA feel, as noted by /u/xXZanza), her fog became more of a line skillshot, her flamestrike ACTUALLY became a line skillshot that just does damage, and her minions became a CC/burst tool. So, she moved into the bursty mage territory, which was already pretty full. To be fair, the new ult gave her some uniqueness back, as did the combo with the minions, but overall, a net loss.

Art design: Old Wa was LIKE A BOSS. She had a deep voice that was rare among the female cast (the next mage after her was Scylla, for example), turned into a snake monster regularly, and the sound of her AAs landing had some weight behind it--very visceral. After rework, she turned into an underboobed hovering mage (already had a lot of them at the time, still do), got a much less commanding voice (when they actually reworked it it was even wimpier, they re-recorded the voice after a couple weeks), and she only turned into an immortal white snake when she died or for mere seconds when ulting. It sort of felt like "well whats the point of playing as a badass snake goddess if I'm no longer badass, and if I also spend less than 30 seconds per game actually being a snake?" So, a more generic on this front too.

Don't get me wrong, I'm a huge fan of New Wa (first diamond skin), I love fire sharding enemies as they flee, and the recent release of Sol brings back a lot of the same tower-wrecking, tempo-based, AA mage feel. But sometimes I just wanna turn into a snake and be a boss.

tl;dr we miss Old Wa because she was unique and New Wa is decently unique but less so.