You can't say "Barth alliance is fine" and expect to be taken seriously. With all respect to Phantas, who I really like, when Gig died serious PVE on this faction died with them, from the same disease that has been eating every guild from them down - no local recruits on a declining faction, and a serious competitive disadvantage for drawing transfer recruits to a declining faction.
It's been slowly getting worse since Vanilla. Pre-TBC you had I think Snitch/Affinity/Dominion on Alliance and Crimson Wrath on Horde all pushing for server firsts. I know the content was something most of us had done before but people were hitting Naxx before the AQ gates were opened in gear that was less then optimal for that tier of content. Barthilas at the time was extremely competitive.
When TBC was released Affinity imploded and transferred to Jubei'Thos to do the whole nova level/man train thing. This left Gigantor as the dominate guild on this realm (latency was just a Horde fluke). Being the top guild they had the option to poach from below and there only alliance competition was Schism post-Sphinx. There was Reincarnation but you needed to eat a special kind of rice to roll with those guys.
Despite the change from 40 -> 25man content you still needed to be in a guild to get access to decent gear. Sure you could pug Karazhan and SSC/TK to some but you needed a semi decent guild to clear T6 content. PVP'ers who wanted to really max/min with that 4pc/4pc combo still had to raid.
Add the changes we've had over the years (10/25 raids sharing the same lockout, heroic gear from each being identical, pvp power being introduced) and you'll have your player base fragmenting all over the place. What were 40 man then 25 man guilds are not groups of 5 - 10 people logging on one or two days a week. The game has changed from individual progression via others to just individual progression by dailies in whatever form.
Look at the number of guild mergers Ensidia merging with Envy. Vodka and Exodus. The high level PVP'ers now transferring to a same realms/faction to arena. Alliance is busy on Frostmourne. Horde is busy on Tichondrius/Barthials. There are huge number of transfers to Malgainis Horde at the moment (judging by auction listing increases by new characters). The players themselves are trying to consolidate.
As your rightly mentioned Gigantor dying is a huge sign that any serious progression at least on Alliance is now over.
I wouldn't be shocked to find 25 man raids vanishing completely in the next expansion or Blizzard having a knee-jerk reaction and introducing something like 40 mans raids back into the mix to try and slow the drain.
Blizzard has accidentally removed one of the M's from MMORPG along the way.