STRICTLY IMHO....two things that really make the decision conclusive - If you are over 5'10" and see yourself doing a variety of mixed terrain I would recommend the 29" wheelset. I have a Trek with my 1st 29er and it rides great. But, if you are shorter than that and maybe under 175lbs, then maybe 27.5" would be better.
The next most important factor are your derailers, expecially the rear one. Not sure what Shimano's latest and greatest is but XT level should be the minimum. That should narrow down your choices.
I ride a hard tail and prefer that to full suspension for all mountain riding and even gravel grinders.
Also, for $1000, you could find a gently used bike that was $2500 new. I have given the local shop a bunch of photographic posters from local events so they gave me a good deal on this trek for $1400 and it was $2200 list.
Also, probably the first thing you want to do is upgrade your handlebars to a wider downhill version.