Interesting, I have noticed a decrease in queue times since 2.5 came out. Although I think a few factors might contribute to the varying length.
Server Limitations:
Like with Amdapor Keep at the beginning of 2.0, it wasnt a lack of people wanting to do it, it was actually the opposite. Too many people were trying to play and all available room for instances was taken up. So even if you had a full party to do and insta-queue, you couldn't until other groups finished what they were doing. Eventually they added more instance servers and this alleviated the queue time issue. To date, PvP has not been overly popular (although I have been enjoying it since its release) so they may not have allocated enough server space for this. With any luck (if server limitations are the issue) if people can continue to have a large interest in PvP, they will increase the server space for PvP instances.
Company Affiliation:
Not sure if this is still the case but for quite a while Maelstrom was the leaders in PvP winning. They were the winning team so everyone was switching to them so they could get wins. Well, with the way that FL is set up, you need to have X people from each Grand Company to be able to compete. Queue times for Twin Badders (err sorry, Adders) was the quickest and would sometimes go through several queue cuycles to the Maelstroms one because they were backed up. I switched to Adders and notied a big difference in queue times.
Data Center:
Also look at what data center you are on. I was on an EU data center because I had friends I played with over there and some days it was a 3 hour queue time. Those were the times where it was peak time for me to play but was like 3-4 am for them so very few people were playing over their data center. Same might go for a JP data center.
Conclusion:
These may not be all the issues or what the OP is experiencing but just a few things to consider when you are experiencing long queue times. I made a few changes, Switched GC's, moved servers, and poof! 10-15 min queue times during my peak play times. In addition, I do hope that SE will open up different PvP games and rules that do not have the GC limitation, I feel this is the biggest cause for any queue wait at all. If you can have the GC's mix for PvP (like in Wolves Den) and have a large scale, fun experience (like Secure or Slaughter) then you will see a much larger base of players doing PvP.
EDIT:
Also, there might be people not using the Duty Roulette (or only using it once for the daily bonus) and only queuing for the Slaughter mode. This could be why you see the 8v8v8 secure Frontlines. I like all modes with WD being at the bottom and Secure being at the top. Either way, if you tick (join party in progress) button and use the roulette, that should increase your chances. If you arent doing ti already or in a party of two that is. Best of luck to all you PvP'ers out there!