I recently got into mountain biking (last summer) and I had to find the answers to all these same types of questions. The answer to your question is not a simple one. You actually have to answer a few more questions before you can know which is the right size wheel for you.
First of all you won't want anything smaller than 26". You won't be able to roll over a lot of obstacles without a decent sized wheel. The benefit of the 26" wheels is that they tend to be more maneuverable, they weigh the least amount and thus roll faster, and if you are not a tall person then the 26" will be easier to find a frame that fits you right.
The 29" wheel allows you to go over more obstacles more easily. They are great if you have long legs. And they are less likely to be suddenly stopped by obstructions.
Then there are the 27.5" wheels. The brand Giant actually did a lot of research on these and have pegged them as the best compromise between the 26" and the 29". They tend to be closer to the 26" when it comes to weight and speed. But closer to the 29" when it comes to angle of attack and the ability to go over obstacles.
Last summer I started out with a 26" hybrid on the trails (yes I said hybrid, it is what I had to work with at the time). I rode with two friends that had real mountain bikes. One had a 26" and the other a 29er. Riding a hybrid definitely held me back.
But I did get a chance to ride both of their bikes and what I found is that it is essential to have a bike that is built for mountain biking when you do this. Both felt smooth as butter compared to the hybrid. Both performed well.
My friend Josh that had the 29er had an easier time going down some rock steps and over some obstacles. But Bill, the one with the 26er, was able to climb more quickly. That said, Bill is also a lighter person than Josh. So that probably added to the differences.
Overall I think the experience with both was about the same. It was really just having an actual mountain bike with strong parts and good derailleurs that mattered the most.
However I will say this, if you are going to spend a good amount of time on paved trails too then you will want to consider the lighter, faster wheels (26 or 27.5). If you are shorter or a low weight person then the large 29ers might require to much of your energy to pedal.
In the end, even though I am not that tall (5'7") I ended up with a 29er that I purchased recently. I did this because I have large strong legs and wanted to go over the obstacles more easily. I think in the end it is more preference though.
Also, Giant has invested a lot into the 27.5" bikes. So they might be worth a look since they have lots of confidence in them.
More info on that: