Yes, Faction Wars needs tuning, but I don't think that's the main problem with the feature.

Glypths are great.  They let us tweak gear and tune it in particular ways, like getting the right speed for clan boss or spider.

Faction Wars is also great, needing to build faction-specific teams let's us use way more of our champions and requires way more work to rank and gear them all.  So, Faction Wars greatly extends the end-game.

I think the problem with Faction Wars is that glyphs are not the right reward.  Making faction teams is a monumental effort and doing all that work for an incremental improvement in gear isn't exciting.

I would suggest making glyph dungeons and rethinking the Faction Wars rewards.  I saw someone suggest something like the Great Hall but for factions instead of affinities; it's not a bad idea.  Maybe better would be some new way to improve a character like scrolls or books but the items are faction-specific.  Maybe runes that can be applied to modify character skills in some sort of talent system.

Since Faction Wars is and should be one of the big end game challenges, the reward also needs to be end game.  After ranking up a character, gearing them, getting masteries and books, we need some end-game way to customize the character further.  I think that's what would make faction wars exciting and worth the effort.