The problem is that everybody's visiting habits are different. If I set the time for longer, we would undoubtedly receive complaints that the new thread indicators don't update fast enough. The only possible solution would be to offer an option for you to adjust the time limit to suit your own personal sufing habits. However, that would require some significant re-work so I can't promise that will happen anytime soon.
In terms of tracking individual threads for each user, that is possible, but highly unlikely, as I would need a about $1,000,000 in database hardware/software to offer personlization that granular.
There are limitations to certain web technologies, and you've just hit on two of them. It sucks because I would like to provide more robust features like the ones you've mentioned, but they just are n't practical from a resource standpoint. Heck, the servers we run now are already hitting 100% CPU usage during certain times of the day as the site stands now.