I'd disagree on making Zephyr more expensive. It's really only a mid-game mech. It disappears from human players' hangars as SP increases and you approach endgame. For it to be more expensive, it would need a longer shelf life.

I now run an endgame hangar, so maybe I don't have as good a sense of what problems mid-game folks are facing, but I feel like the bigger issue would be all the AI Zephs & Surges, especially since the AI Zephyrs all have their freeze radius boosted. All the Zephyrs with Longarms or EMRs equipped are AI not human players (ditto Surges with Stasis/Thermal Beams) Switching out the AI Zephyrs with a different bot like Guardian would help a lot on the freeze wars issue. 

Yes, as a mid/endgame player I see tons and tons of zephyrs everywhere

What's your SP number? By around 5500 Zephyrs rarely appear in human hangars. It's only bots that run Zephs.

I'm almost at the end of the progress path, but my hangar is is still somewhere around 2300 power.

Idk about that. I can't remember the last time I played a match with the opponents having no Zephyrs. Even not counting the AI, Zephyr + Missile Weapons/Gauss Rifle is basically a Meta at this point. I do believe there has to be some nerf of sorts because like OP mentioned, any team with EMP Mech numbers is very one-sided

I realize there is no standard definition but I'd say endgame really starts around 5200sp hangar strength. And human-piloted Zephs are quite rare at that point. Their health is too low and they are too slow, so they can't really punch through and attack and they too weak to be a sniper. Basically they are an ambush mech only and the game is more aggressive at that point with better mech options available. That is also why Javelins are more uncommon as they are really an ambush weapon (although now that there are 12 & 16 versions that might change idk).

Main thing is I wouldn't bother taking your Zephyr past R6, especially if you have AT10s. It's not worth spending A-Coins to accelerate Zephyr past that. It is worth taking it to R6. It can be a pretty dominant mech in early & mid game, but unlike Killshot, Panther or Guardian it doesn't hold its value long-term.

Well then they should at least tone down the usage of zephyr in bots

All my bots suddenly seem to be bastion and brick house.