If you read the summary on the Ascend site for the S2 EXv2, the upgrade makes the speaker warmer/fuller than the S2, along with improving the bass. One of these days, I plan on upgrading my S2's to the EXv2 but not in a hurry as using them for surrounds (and I'm mostly music).

Yes, there are at least two Horizon upgrade kits - the V2 (cross-over only, I'm fairly certain) and ELX (cross-over, two LX drivers, 1 EX driver).

I'm not sure why the S2's are fatiguing & sound bright in your system and/or room. As you mentioned, maybe it will take some more time to adjust to the sound difference from your previous Polks. Also, did you run room correction or are you using any of the Yamaha sound "modes"? Maybe that's impacting the sound negatively.