I've been comparing my 29er HT (Kinesis FF29) with my 26" Full Suss (Giant Trance) and as with so many things in cycling, it seems to be swings and roundabouts. There are things about each bike that I love and times when each bikes seems to be the absolutely perfect choice. But there are also times, often on the same ride, when it is quite definitely not.
The HT has that wonderfully efficient feeling. On a long or steep but not too technical climb it is amazing. I've ridden up climbs that I've never come close to getting up on the full suss. But I've also failed to get up some more technical climbs that I can do on the full suss, simply because I got knocked off line.
Similarly, on the way down, if there is a smooth(ish) line that can be taken the HT can be huge fun. Being less isolated from the trail allows you to really feel the line and put the bike where you want. But when there is no smooth line things can get unpleasant. I've found myself just wishing for the descent to end in some cases where I know that I'd just be blasting down with a grin on my face on the full suss.
There are lots of other pros and cons of each bike, but with most of the others it's hard to tell whether it is the lack of suspension, the different wheel size or the different geometry that is making the difference.
In general (and for me) I think the HT favours shorter more active rides or longer rides with a large amount of non-technical riding (roads, forest tracks etc). If I can keep attacking the trail and stay on top of it then it is great fun, but once I get tired I can quickly get fed up of being knocked about all over the show.