Many of those ideas have great merit. I too had the problem with security spikes and tunnelers, I just sold them every time I received any.
The skill sets were acceptable, but need a great deal of refining to be excellent. I'd go more in-depth with the skills, and allow them to play a greater role in the game, as well as do more diverse actions, more frequently.
The only time security really made a difference was around Taris. After that, I found myself using it on VERY rare occasions. Repair was useful for HK-47, but other than that I never found a need to repair all the droids found in the game. Computer Use was one of the better skills, but I found that I was using it far too much in the game, compared to the other skills.
Hopefully the skills in KotOR 2 will be much more refined and useful. :ph34r: