How much have sub-woofers changed over the years?

The Rel is a tighter more musical sub, yes. I've sold both retail over the years. However, placement, setup, calibration and tweeking is going to amount to FAR FAR MORE than simply weighing one sub over another in this case.
Personally, I like the Rel's for more subdued music dubties, as with the F1200 really. Both can be overloaded and or shut down if you drive em too hard for movies.(also, how big is the room/space).
If you're looking for improvement, where are you looking improvement for? Are you trying to improve output and dynamics, or are you looking for more accurate musicality.
Dunno anything about your situation really. But I'd recomend a sub that does supperb double dubty for both music and HT for a song! And that's the Paradigm Servo 15. Also, the M&K MX200 and above, but they're pricey for what you're getting I think. Really, the MX350 is more a closer match for the SErvo15, or maybe the MX5000 M&K sub.
I really don't see the hype on these Rel Subs for serious HT applications, only more subdued music listening. I think there are better HT/music subs out there.
All that being said, 75% or more of your performance and effectiveness of your sub is going to be placment and finetuning FOR CERTAIN! This is where everyone fall short mostly.
So, to answer your question about changes in sub's, I'd say they haven't changed enough to cause a revolution or anything. Bigger subs can belt it out easier still, while smaller subs need more watts to try and keep up(often at the expense of accuracy). Also, subs with inherently tigheter "Q factor" are usually more musically accurate, while more dedicated HT subs often sacrifice accuracy for output. Still, with the advent of servo's and such, nothing has really changed. A good push pull design, sealed acoustic design, a well integrated bandpass design, transmission line, you name it, all can be designed with very good effectiveness for what's needed if DESIGNED CORRECTLY!
The Rel's are good subs, but depends on the application from my experience. I've sold Rel's at 2 high end stores now, and know what they can do, as with other brands.

I'm running a velodyne ULD-15, 400 watt servo with brand new soliloquys and couldn't be happier. All that has changed over the years is that Velodynes have gained more wattage and performance for the money. A used sub for probably 1/3 the price is a great deal and an awesome performer!

I have a Velodyne F1800X (750watt version of the F1800) on my video system and placement and configuration really does make a difference (I put mine on a Sistrum SP4 stand and the bass tighened up signifactly in my system). But if you are looking for more output! Get another 12" Velodyne and go Stereo subs and place them on the same wall (not next to each other but othe either side of your center or corners..) This dual sub configurations helps cancel out nasty room nodes... Plus Stereo bass rocks! (I use to have 2 VMPS subs but the size made me get rid of them...)

I use a REL Strata II for a SET tube system and also have used it with a dedicated home theatre system. It works at least as well as the Energy subwoofer (like the top of the line Sunfire 1000 watt sub; small things with big performance) on home theatre stuff and excels at integrating with the two channel system speakers which are Galante Rhapsody high efficiency monitors.

If you want real home theatre noises find a used McIntosh passive dual 12" subwoofer and use it in conjuntion with a very powerful solid state amplifier. A neighbour uses that on his X.1 channel and it moves mountains.

Honstly, if you are serious about improving your system, I'm most certain there are better ways than simply focusing on possibly upgrading your subwoofer.
For instance you use B&W nautius speakers. Which ones?
Regardless of which they are however, you should be setting them to crossover at abot 80hz on your receiver, period. ESPECIALLY SINCE YOU USE A RECEIVER(and I'm very familiar with the B&K line, and have sold it retail), you need to take advantage of the bass management, as your passive system and receiver combo demands it. Also,speparates, or at the very least adding a multi power amp, would be a big improvement after that. The output from the amps in your receier aren't goign to deliver the current a dedicated amp would. You'll notice big improvements in not only dynamics and power, but every other area with this upgrade.
Then, your setup and calibration of the system is of utmost importance as well. For instance, are all your speakers placed where they're coupling to the room well for excellent frequency response?...at the crossover?...is the sub in phase wih all th speakers from where you sit?...hows the levels?...acoustic?...do you sit close or far from your main speakers in relation your ceiling height and wall proximity?...against the back wall or more out in the room?...where exactly are you crossing over your speakers, or are you running em all full range?...How big is your room/acoustic space and is it open to the rest of the house or attached spaces?(sub requirements would vary here)
I guess what I'm saying is that there are many many other considerations and probable compromises that are keeping your systems potential at bay. The sub is only a part of the equation for excellence and success. Infact I find most peoples mediocrity, even with higher end gear and potentially excellent tools, stems from lack of knowledge, improper setup, integration, execussion, and simply too many variables that are not adressed properly for best results (compounded with multi channel systems BTW).
Most simply don't have a clue...they only read the articles and hear a speaker or two. They then go buy what they think will give them killer sound/video and are dissapointed at the results more often than not! There's WAY more to it than gear.
For instance you've got some good tools in the B&W speakers, with a much better than average receiver. Still, I've been down that road enough to understand there's a lot of ways to make gear like that sound very marginal...and only a narrow path towards getting stellar results in any given room/setup! It's all in the know-how...