Openings, they are the enemy
There were some other threads where other folks were debating with me whether it was worth getting a higher output sub. Some folks kept saying that the room size wasn't all that huge (3000 cubic feet). That's a "large" room by THX standards, so already, I was leaning towards more output. Then the photos came in and showed that the room was actually entirely open to a hallway and that hallway was open to...who knows what.
It's so tough to try and stress that folks have to consider ALL of the air. Anywhere that the air can move, that's part of your "room". The subwoofer makes no distinctions. Air will escape and more wherever it can, so a simple 14' x 20' room can seem like no big deal, then you discover there are openings to other spaces in the house and suddenly the actual "room" is massive!
The VTF-3 MK3 is a very capable sub. But it's still just a 12" sub with a 350 Watt amp with a large box and quite a bit of port area for low tuning. It's powerful. But it still has its limits! I've talked to people here and elsewhere who've made SVSound PB12-NSD subs completely run out of steam in "rooms" that didn't seem all that large until all of the openings were discovered. Heck, I've met people who've made PB13-Ultra and Seaton Submersive subs cry uncle!
I do completely agree though that you need to revisit your "crawling for bass" and then bust out some measurement gear and REW software. I noticed in your pictures that you first had the sub positioned in front of the primary seat. You need to physically move the seat out of the way and get the sub right where you will be sitting to do the "crawl". 6 inches can make a noticeable difference, so you've got to have the sub more or less exactly where you sit. Then go crouch and listen in EVERY conceivable spot where the subwoofer could go. That might be in some really odd spot that you didn't originally consider. But if the sub CAN go there, have a listen at that position. You can often discover a very good spot in your room that you wouldn't have thought of before.
If you want to save a bit of time, turn YPAO off and manually set your speakers to an 80Hz cross-over with all of the trim levels set to zero. Play the pink noise from your receiver and use a basic SPL meter to get the subwoofer's output CLOSE to the same volume as the speakers, and get them all generating somewhere between 75-85dB output with the pink noise. Now put on any THX certified DVD or Blu-ray, go the THX Optimizer setup menus and go to the last Audio Setup test, which is a 200Hz - 20Hz sweep tone. Put that chapter on repeat so that it just plays over and over while you are "duck walking" around to all the spots where the subwoofer could possibly go.
With this setup, you'll have both the speakers and the subwoofer playing, so you won't have to mess around too much with the cross-over later. With the speakers playing down to 80Hz and sloping off below that, you have to basically consider them as additional subwoofers from around 160Hz down to around 40Hz or so where both the speakers and the subwoofer are contributing significant output. If you do the "crawl" with only the subwoofer playing, you will sometimes find that when the speakers are playing again, the cross-over region is all mucked up due to cancellations between the speakers' 40-160Hz output and the subwoofers' 40-160Hz output. So you can save some time doing it this way.
Now you bust out the measurement gear, set it up at your primary listening spot and get yourself some pretty graphs with REW!

You can try running YPAO and measure again yourself to see what the heck it does. I've never been impressed with YPAO's results, so I typically turn it off!
If you can't get away from some large peaks no matter where you place the sub, then you'll need an outboard EQ unit. REW is set to work with a number of EQ units automatically. It will literally figure out the parametric EQ settings and automatically adjust the EQ unit for you! So that's a very nice feature

Check to see which current EQ units REW supports.
If you have some large dips in the bass, well, you're up a creek. You can't "fill in" dips with EQ. Dips are caused by cancellations. Making the output louder won't do anything. The louder sound waves will still cancel each other out at those specific frequencies! You can fill in minor dips of like 3dB or something, but not much more than that.
Dual subs have to be properly placed. You're basically creating a "phatom sub", much like how your Front L/R speakers can create a "phantom center". The "phantom sub" allows you to "place" a subwoofer somewhere that a physical subwoofer cannot go - like somewhere out in the middle of the room. But you can still get some very strong cancellations. If the two subs, plus the room's acoustics, happen to create a big dip at your seat, well then you're still screwed! And you will get some big dips somewhere with two subs. It's just a matter of getting the two subs and your seat positioned so that the big dips don't happen at your seat!
With 4 subs, placement becomes less critical. You still can't place 4 subs totally randomly and expect perfection, but it's a lot less picky with 4 subs and you can get pretty flat response at quite a few seats without a ton of hassle. Funnily enough though, 4 subs can actually measure as being
quieter than two subs or even just one, lone sub! Having 4 bass sources all playing the same sounds at the same time means a ton of sound wave interference. That's what allows you to get such even bass response at so many locations! But it also means that the overall level actually gets quieter, which is something that most people don't expect!
So 4 ULS-15 that are spread out around the room? No match in terms of just peak output for just a lone PB13-Ultra. But WAY smoother frequency response at multiple seats. And if you stack some ULS-15 subs, now you're boosting the output. 8 ULS-15 subs is not crazy at all! 4 stacked pairs gets you very even, smooth bass throughout the room plus lots of output. Of course, 4 PB13-Ultra costs roughly the same and 4 PC13-Ultra cylinders are less