The idea here is to do away with the 'classes' and completely open character creation and development. I do not think the ideas here would revolutionize the game, nor would they change the game too much from what it is. By and large the mechanics would remain the same.
Firstly all skills would need to be marked, or separated by their type; science, tactical, or engineering.
The player can then choose any skills from any group so long as they meet the prerequisites, which is not too different from what it is now. Of course, as they do now, the abilities of Bridge Officers, Kits, and personal abilities are dependent on the players skills.
When a re-spec is done, it simply removes all the set skills allowing the player to reassign their skills completely (e.g. previously the player was focusing on science skills, now they want to re-spec to focus on tactical skills with some science skills to help out). And since there would be no classes, there is no worry about choosing the wrong class and wanting to change it latter, a re-spec token would take care of that.
Kits would have to be handled differently. All kits would be open to any character so long as that character meets the level requirements and any other prerequisites. If a player focuses on sci skills, it means the science kits will be more effective, however that player would have the freedom to switch to a tactical or engineering kit as they need. A player focused in science skills will make better use of science kits of course. Maybe high level skills could unlock special attributes in some kits.
The ability for any player to use any kit would truly open up some interesting group dynamics. A science skilled player might find themselves playing in a tactical role for example if her group lacks fire power.
As for click able abilities that characters gain just by advancing their levels, why not create a Power tree an when players reach a certain level they get a point they can use to spend in that tree either to improve powers they have or to purchase new ones. Again a player should be able to purchase any skill they meet the prerequisites for with no bearing on 'class'.
Overall, these game modifications would do away with the narrow class definition – sci/tac/eng, and
allow players to customize their character in any way they like. They may choose to make focus completely on one type of skills, but they might also choose to mix it up and create a character that can truly fit a number of roles.