One of the biggest gripes with doing an STF is not really the difficulty as much as the respawn and it's rate. Thus I propose two different ideas to counter this..
1) No Respawn... The simpliest idea is to stop respawn period, thus when you clear a section it stays cleared. Now this will mean making the fights for each section more difficult but rather than using more enemies why not use smarter enemies. Let them setup crossfires and such, even built a real defensive position if they are able to within the sotry line.
2) Re-enforcements, NOT respawn.... The idea here is rather than the respawn dropping in right where they where before you have re-enforcements coming from a deeper area. These are enemy troops rushing forward or ships warping in to assist their brothers. In this way clearing an area stays cleared but there is the threat of a counter strike on the way. With this in mind players will not just advance but be forced to advance with caution and setup peremeters to prepare for the coming counter attack.
Looking at the current mission design it would appear to me that either of these designs would make the STF as challenging but in a manner that players would feel more like they could develop counters for. Both would still require teamwork and tactics.
The easiest solution would simply be to double all the time limits of things and reduce the number of spawns by about 25%. The gimmicks are the gimmicks and changing them would take some time and effort.
They got to do something. 5 from my Fleet could not finish The Cure yesterday. Respawning Elite Tactical Drones just took the fight out of us after 8 hours. No wonder no one wants to do The Cure more then once. Just not fun. Though we did have issues with players leaving after 4 hours too.
Cryptic has completely failed when it comes to the STFs. They are horrible from a design standpoint being no fun at all. If I am not mistaken they serve no purpose whatsoever since there is no unique loot or reward that they give out.