Hi Joe,
I have a pair of original Super 3's identical to yours (mine are light beech veneer). Everything you described is true, both in describing their strengths and their weaknesses. I can offer this:
1. If you haven't upgraded the drivers you can swap the Fostex drivers for the latest RS5 drivers. It is a modest cost (less than $200) and takes about 10 minutes. It is not a subtle upgrade. It will be more efficient, produce better highs and much more bass.
2. The wide baffle provides better lower midrange response than the newer, narrow baffle models. That being said, they do well with wall reinforcement. The shallow cabinet helps with that.
3. There are a number of subwoofers that will work really, really well with the fast RS5 drivers. Omega subwoofers are a natural fit. A number of us also use Rhythmik servo subwoofers that use GR Research lightweight paper driver(s). Many people agree that stereo subwoofers are superior to a single subwoofer.
4. Even with a subwoofer you may not find a single RS5 speaker as satisfying as you would like. Much of what we want in bass reinforcement is actually mid to upper bass. The RS5 driver begins rolling off slowly below 500hz, which contributes to its slightly thin sound. Louis addresses this in some models by paralleling an additional driver ("1.5 way") below 500hz, adding the missing fullness. The two drivers in parallel have a similar radiating area to a single 6.5" driver. These 1.5 way speakers are in larger cabinets as well, even the small monitors. The Super 3 HO is about 20% larger than your current speakers.
If it were me I would stick with monitor speakers. You own an expensive set of stands already that will work with a couple models that would give you better bass response. As RDavidson pointed out, the Super 3 HO would be about the same size as your current speakers but would offer more efficiency and better bass. I would also consider the Compact Alnico Monitor, which is a similar size and maybe has a bit better bass than the Super 3 HO. They are within spitting distance of each other in cost (but both a bit more than that a Super 7Mk2 Monitor). The wide baffle of the CAM would make it look and behave very similarly to your current speakers, only better in almost every way (assuming you still have the Fostex driver).
I own a number of Omega speakers based on the RS5 and Alnico drivers, starting with the same model as yours and adding different models. Some observations:
1. Super 3. I replaced the original Fostex Fe127e with the RS5. This is hands-down the best bang-for-the-buck upgrade you could ever do. Right out of the box with zero break-in the Omega driver smokes the Fostex in every way. If you wanted to improve your speakers without major commitment this is where I would start.
2. 1.5way RS5. I am testing out a 1.5 way version (unofficial - so really Outlaw) of the RS5 speaker for use as a center channel. It really sounds like a RS5 with more bottom end and drive. If you know you like the RS5 you will like the 1.5 way.
3. Super Alnico Monitor. This is the larger version of the Compact Alnico Monitor. This is a much fuller sounding driver with better inner detail. However, IMHO it is not as pure or extended on the top end. But combined with your Scott 299 it would probably be killer. It is not what I would call a driver with the deepest bass, but I can locate the rear-ported cabinet closer to the wall to fill out the low end in a smaller room.
TL;dr: If it were my money the first thing I would do is upgrade the drivers if it hadn't been done already. The speakers would be that much better in the office system. Following that, if I were going to place the speakers in the traditional "audiophile" position out in the room I would probably choose a Super 3HO. If I were placing them a bit closer to the front wall, I would probably choose the Compact Alnico Monitor. I haven't experienced the RS7 drivers so can't offer an informed opinion on them.