First things first.....Trek, Specialized, Niner and Giant all have different geometry. Why? Well....that I don't have an answer for but I do know that each company tries to "tune" the bikes to certain rider sizes and shapes. Take it easy....I am not judging the designers and engineers that create these machines we love....all I am saying is that the broader range of people a bike can fit the better. That is why we have small, medium and large bikes....with a billion different stem and handlebar combinations. So...back to the point...while I may feel comfortable on a Large Giant the same might not be said for a Large Niner. I am sure they are close...but the differences can be subtle enough to merit a change in size. Find a geometry that feels right and tweak the bike from there.
Size matters? Wheel size? Really? Ok, so now we have a 26" wheel, a 750b and a 29" wheel. Allright....are there differences....well...yes....but as I explained to my friend I will now explain to you....as the way I see it. The trend is surely headed towards the 29er crowd. Bigger wheels put the axle another 1.5 inches higher and make those wheels roll over obstacles better. Awesome. But....it takes longer for the wheels to get up to speed.....so.....trade off? Doubt it....I think it comes down to more than just the wheel size itself....but the actual rider....size...and riding style. Me for example....I am 6'1" tall and weigh in around 250 (ish) and most of my weight is from the waist up. In my eyes....my center of gravity is pretty high already. So...putting that COG another 1.5" higher has advantages when rolling over log piles or taking a step up....but does it help in the corners? How can I hold the bike down when my ass is another 1.5" higher on off the ground and I need to hang a right? Well.....simply put....riding style. I would ride a 26" wheeled bike differently than a 29" wheeled bike for that simple reason alone. They handle different....rotational weight is different....COG is different....the bike is just different.....almost as different as a hardtail and a full suspension bike.
All I am saying is that each bike, tire, shifter, pedal, wheelset, and component will treat a person differently. My friend Dan S. and I are the nearly the same size and build. He is a stronger rider than I am....hands down. If we had identical bikes he would crush me on that aspect alone....but our riding styles are different too. I take different lines than he does. I clear some sections....he clears others. Each of us will handle the same bike differently and ride differently no matter what. One simple change...such as tires....can change the entire way the bike rides. Dan made a comment last time we were out about how differently a Giant Trance and a Niner handle. Different bikes.....wheels....components. Even if set up exactly the same they would be different.
In general.....what it comes down to is simple. Ride what you like. Try a few different brands of bikes, tires, shifters, shoes and whatever else you can think of. Each brand offers different things and different feels. What I like may be way different than what you like. What my friend likes I might hate.....it is the nature of the sport we love.