This is the way i see it.
Mazda had both the single runner manifold and the dual runner manifold available when they built the protege.
They know the difference the manifold makes in both low end and high end power. They chose to go with the dual runner design for the protege becasue it provides more power and a flatter power band where as the single runner provides more highend.
Dual runner is better for daily driving, more power below peak but has a lower peak
Single runner is better for high rpm driving and FI applications or all motor builds that flow alot more power then stock.
Someone with a stockish motor that upgrades to a single runner may find a noticable loss of low end and midrange power.
IF you decide to go to a single runner manifold you may want to get a lightened flywheel and lightened pullies to get back some of the lost low end.
But low end, off load driving doesn't matter. You don't USE power down there as it is... when you are cruising who cares as long as you can get the car moving. Everytime you decide to have some fun with the car, overtake, climb a hill, or race on the track, invariably you are using top end, be it a daily driver or otherwise. If you lack the grunt, you back it down a gear to get the car back into a usable power band.
The loss wouldn't be so noticable as to make the car difficult to drive around at low RPM. You may even find a marginal improvement in fuel economy by dropping a little low end.
Further to that, the 626 is a family car, and mazda saw fit to give it a single runner manifold. 626 drivers don't complain about a lack of low end power.
The reasons why mazda gave us a dual runner is likely to be to provide better fuel economy on a slightly more powerful motor, than to give us a flatter power curve.
Also, the standard manifold is *incredibly* lossy. I've seen numbers - can't remember them, but Kooldino will vouch for just how lossy the dual runner mani is. the way it is designed delivers vastly reduced air flow. The 626 mani may not be "tuned" for low end, but it will most likely flow more air at low RPM and thus make up for some of the loss.
Yes, to make the most out of it you will want some form of aftermarket management (the 626 computer is obviously tuned specifically for this manifold, the OEM 323 computer isn't), but the benefits of doing this far outweigh any perceived disadvantages.
As stated before, the LATER you can achieve peak torque in the rev range, the GREATER the acceleration because of an improved ability to leverage gearing - the car will accellerate faster by pushing the torque band further up the curve. You are worried about a "feeling" of lethargy.... in real terms its not there.