There are some die hard 29er guys out there who might disagree but I don't think that 29ers are neccasarily the "future", they're just a different riding experience. There are advantages and disadvantages to a bigger tire. It's easier to get more speed on a 29er and obviously the bigger tire makes it easier to roll over bigger obstacles but you get a lot more balance on a 26 and there's also a small weight advantage with a smaller tire. Also, and this is something that has started to become less of a problem as 29ers become more common place, if you ever decide to make upgrades, you might run into compatability issues with a 29er.
Most bike companies (ie Trek, Giant, Gary Fisher, Specialized) all have great entry level bikes and for the most part the differences between them boil down to the components and geometry (geometry determines how they handle when they climb, descend and ride on flat terrain). Determining which frames geometry is better is largely a matter of preference and the best way and really the only way to determine which is best for you is to test ride them. Most of the components (derailleurs, cranksets, shifters) are either shimano or sram and from my experience, the quality between the two brands is very comparable although certain people tend to perfer one brand over the other (again personal preference/past experience). For example, the Yeti 575 has two models for the exact same price, one with SRAM components and one with Shimano.
Since personal preference plays such a big role in determining which bike would be best it's hard for me to give you a good reccomendation. Most of my friends who ride ride bikes that they have spent atleast $800 on and I've never ridden one and thought, "this bike is garbage" or that I couldn't a have a great time owning it. Obviously there were some that I preferred over others but it all depends on your height, weight, the shape your in and the way you ride. I ride a Trek Fuel Ex 6 (if I remember correctly MSRP around $1500 but I bought it from a coworker for $600) and I absolutely love it, but just because I love it doesn't neccasarily mean that you would love it too. The best advice I can give you is to test ride 3-5 bikes in your price range and then make a decision based on which one felt better.
I could be wrong but I believe the Shimano hierarchy (from the bottom up) goes Deore, Deore XT and then XTR. I know those aren't the only components Shimano makes but those are the ones I've seen the most on MTBs. If someone doesn't give you a different answer here on the site the guy at your LBS might be able to give you a more accurate answer. That being said, another factor you should consider too (if you have more than one LBS) is customer service. Make sure the people who work there know what they're talking about.