To answer your questions:
The 999S Comes with a termi exhaust, correct?
The stock exhausts are Termi, but for regular street use. They are like that for all Duc Superbikes. The 999s is no different. At least here in the US, it is not equipped with the "for race only" Termi exhaust that is commonly purchased after-market.
... will that exhaust fit on an 04 749?
It depends on the model year of the 999s. The early 999s bikes did not have a "deep sump" engine, while the latter ones did. I am not sure whether the deep sump engine was introduced to the 999s in 2004 or 2005.
Deep sump engines will require a lead exhaust pipe that is designed to go around it. So, exhaust systems designed for deep sump will not fit those designed for non-deep sump and vice versa.
No 749 is equipped with the deep sump engine (except the R). Even if you did find a 999s with non-deep sump pipes and installed this to the 749, it will fit, but you will be replacing the exact same parts. Needless to say, there will be no value in doing such a thing.
I know the ECU might be different, so I was thinking to use a power commander III, but with the actual physical fit of the system work?
The only ECU you can 'properly' install to the 749 is one that is designed specifically for it, if not, just use the stock ECU and install a PC3 to optimize fuel delivery.
Is the Termi system that is used on the 999S the same as the 1/2 system that I would buy aftermarket for my 749?
No. The Termi half-system you purchase as an upgrade for the 749 will have a pipe that is designed for regular engine, no deep sump (the 999S stock system may or may not be for deep sump, depending on model year).
Also, the Termi Half System will not have a catalytic converter, which is built-in on all stock exhaust systems. Thus, Termi will supply a new ECU specific to the bike model that comes with the purchase of a new half system. That ECU is provided to optimize fuel delivery without having to make any further fuel adjustments, purchase PC3 or dyno-tune.
Lastly, the Termi "after-market" exhaust cans are not the same cans on the stock Superbikes. This is what gives it the louder sound and free-flowing characteristics over stock.
Does it sound the same and offer the same weight loss as compared to the stock system?
No and No. The stock exhaust on the 999s is exactly what it is: STOCK. The true after-market Termi race exhaust systems, whether half or full system, will have substantial weight savings over stock, has a huge sound difference and will provide performance gains as well.
As a side note, unless you are out to squeeze-out every bit of hp out of a 749, it is best to go with the half-system, as the performance difference between "full" and "half" might not be significant enough to warrant all the extra expense.
If you only are going for the sound and looks, it's best that you just find a Termi "race only" exhaust (no pipes) and install that into bike... but that exhaust can has to come from a "half system" only (not full system ... it will NOT fit otherwise) ... this is probably the most cost-efficient way to enjoy the sound of a Termi on your bike.
Hope that helps.