You asked for it 
I’m just starting this process so I’ll tell you what I can. I’ve ridden a Softride Rocket TT7 for the last couple years; I have a history of lower back problems and that’s what led me to buy it in the first place (I didn’t own a true Tri bike before). I have no complaints with the bike and do really enjoy riding it. Recently I bought a used Yaqui Carbo frame because I knew that the previous owner and I had very similar measurements. Besides I agree with his well known opinion of bike geometry and figured I’d like the frame (guess who?). Why did I buy the Yaqui when I liked my SR? - honestly just for something to tinker with. I wanted to see for myself how I would like the Softride vs. a well built, good fitting traditional frame. My intent is to do my own tests over various courses to compare comfort, speed, etc. between the two frames. Not a true scientific test and no goal other than to give myself something to do for fun during the off-season.
So I built the Yaqui up from scratch and ended up with a very nicely equipped bike. Only the brakes and handlebars really differ from my Softride, so I think the bikes are comparatively equipped:
General Feel: The Yaqui is fun to ride. Not that the SR isn’t, kind of like a Caddy vs BMW. Not necessarily faster and somewhat hard to explain, let’s just say the Yaqui has a more nimble & lighter feel (I haven’t weighed them). There are some other little things that are hard to quantify, stop at a stoplight and you don’t have the beam riding your crotch. You can more easily mount and dismount because you don’t have that unloaded beam sticking up to highstep over (minor I know, but I’ve noticed it). I feel like I climb better on the Yaqui, in fact, just this week, I set a personal best on my 7 mile “hills” loop, beating my previous best time by 2minutes (note: my best time was set on my road bike!).
On the other hand, there is no question that you do definately feel the road more on the rear of the bike. Bumps that I never knew were there, all of a sudden are felt. It’s not too bad with 23c tires at 120psi, but if I throw on my Hed Alp Tubular rear at 140psi, it becomes more noticable. Honestly it hasn’t bothered me thus far, but I’ll admit that I’m only doing short course stuff this year and haven’t been riding much over 30-40miles per ride. I’d bet that the cumulative vibration will be much more obvious as I get my mileage back up.
Fit: The SR trends more toward a road geometry (at least on the large 700 size)-just look at the headtube length. The adjustability allows you to set the saddle anywhere you want, but I believe there are handling drawbacks when you get too much weight forward. I immediately set up the Yaqui with 6cm more drop between saddle and handlebars then the SR and I don’t feel like I lost anything in terms of handling, stability, etc. I do need more comparative experimentation in this area though.
Running off the bike: Again, I’ve only had the Yaqui built for a month or so, but I honestly haven’t noticed much difference in the run portion of my bricks. I did back to back sprint tris one week apart (first on the SR, second on the Yaqui). When riding the Yaqui, I posted a better bike ranking in a more competetive field and still ran 4 min faster off the bike (in a 5K!!). My back actually was bothering me coming off the SR, but not the Yaqui…
…But PLEASE don’t take the above as anything definative I could give you the race results & course profiles and you could pick it apart to mean anything you want. The SR race was my first in almost two years. My wife & I have a 2 month old baby & a 3 year old, so my training has been minimal at best. These were only sprint tris, the courses were different and at that distance anything can throw you off. This is only one datapoint and the improvements in that one week are almost certainly largely due to getting comfortable racing again. it would be stupid for me to say that I definately run better off one bike than the othat at this point. What I will say is that for short distance stuff I haven’t yet noticed a significant difference.
So this is a very long way of telling you that I have a lot of experimentation to do. My initial impression is that I probably prefer the traditional bike for short distance stuff, especially hilly courses. There is something about the traditional bike that makes me feel more solidly connected to the road and I like that. However, I have yet to generate actual numbers to quantify the results and can’t yet make a comfort determination for longer distances although I won’t be surprised if I prefer the softride for those 100milers.