Also, if you love a certain bike, and only one or two components are putting you off remember that it may be worth it to go for it, and replace the few things putting you off when you can.
I would say something that I didn't expect to be doing much with my bike was jumping stuff/drop offs. I started doing some small stuff, and really like the feel of being in the air and hitting a nice crisp landing. I'm noticing with my bike that I bought mainly for XC type stuff that the frame is great for speed and comfort over long distances, but is a little bigger than I would want for doing jumps/drop offs over 3 - 4 feet and more risky stuff. However, the compromise works out for me because I do ride a lot of miles, and only 1/4 or 1/3 or so is actually somewhat challenging.
So, definitely try to think about what you will be doing, and make sure if you want to be hitting bigger stuff that you get a small enough frame. If you don't want to get too crazy a larger frame may be more comfortable.
I ended up getting a close out 2010 Felt Q620, which is way below the $1000 mark. This allowed me to save a bunch of money to replace some crucial elements (I.E. fork, tires, saddle, pedals, stem) to improve the ride substantially. The end bike is right around $1000, maybe a little higher. I can say I am quite happy with it, and you may want to check out some of the Q series.