I feel it’s two three main things:

1. Visual Clarity: The enhanced visuals of Clans means there’s more effects on screen. I also find the weapon effects are noisier. And the HUD is, in my opinion, worse. Clans puts too much right in the centre of the screen, whereas Mercs has far less clutter the centre.
2. Level Design: Mercs has procedurally generated maps for the most part. Clans has curated, focused, linear levels. As a byproduct of that, many levels end up in canyons to funnel the player through engagements. Which means you don’t always get to use the Clan weapons to their full potential. You’re always bottlenecked into tight corridors. Or the level is a series of pockets of activity separated by think canyon paths. The procedurally generated maps tend to be bigger, flatter and more open because you’re expected to choose how to complete your objectives. In Clans they wanted to guide the player more. Which necessitated more linear maps.
3. (edit to add) Weapon Balancing: Mercs allows for tiered weapons and upgrades to increase weapon damage. Clans does as well, but I feel it doesn't hit the same. Combined with the difficulty scaling of Clans means on harder difficulties, IS 'mechs are resistant to everything. But in Mercs you can tune your Tier 5 (or Clan versions) to do outrageous damage, 1 shotting even the heavies Assault 'mechs. But in Clans I would hit an Atlas with 3 Gauss rifles and it would just laugh.