So when I used to spec for any build (pre-new skill system) I always spent about 7 skill points in teir 1, 2, and most teir 3 skills. The reason being that the added 1.5 or 2 extra bonus didn't seem worth the skill point expenditure to max out the skill to 9.
Following that logic I applied it to the new skill system, where ALL the skills only improve by 2 points after you get it up to 7. Following this system, I got up to VA with 450 extra points that I just spent on a teir 3 skill.
So I was able to use all my points and I had a nice spread out skill point allocation with 7s in nearly every skill. The skills I tended not to improve (due to lack of interest or importance) was hold buff/resist, energy drain buff/resist, gravitational buff... pretty much most 'specialized' science skill buffs.
So just to test out the new skills on space combat, I went out and did 'night of the comet'. The reason I chose this mission was because it is one of the MOST challenging space missions I have ever soloed. When you pound on driffens comet and get 4+ D7s all attacking you at once it becomes a desperate fight that is pretty challenging to overcome.
DISCLAIMER: I realize that this mission has an 'easy' way to complete it... by destroying only a few peices of the comet at a time and then disabling 2 d7s... going back to the comet... so on and so on. This was just a 'stress test' to see how effective the new skill points were.
Normally I would get my @$$ handed to me in this mission with 6 D7s all shoving disruptors down my throat, especially when I am using a prometheus (No multi-vector). Not only did I survive, but I noticed a VASTLY increased manuverabillity and crits landing almost constantly. I scattervollyed and torp spread the holy bejeezus out of all the D7s with relative ease and didn't dip below 50% hull the entire battle!!!
Just to make sure it wasn't a fluke I busted out my cruiser Klingon in a retrofit VorCha, and spent my skillpoints in the exact same way. I had Fire at will 2 and torp spread 1 and the same result. My beams were blasting away at the D7s and comet fragmets so fast and furiously... I couldn't even keep track of what was going on. The battle was over before I even realized it and the mission was completed. I also noticed the VASTLY increased manuverabillity in the VorCha as well. I was flying CIRCLES around the D7s faster and tighter than I EVER have in any cruiser I have ever captained.
I have to say that despite the large chunk of players barking about how 'nerfed' the new skills feel, I have noticed a DRASTIC boost to speed, crits, overall DPS, and manuverabillity. I can't say I see any cons to the new skill revamp. I would love to see slightly higher numbers, but really who wouldn't. LOL
So to recap, I used the same exact skill point allocation for both a FED ESCORT, and a KLINGON CRUISER... and they were both equally effective and even MORE survivable than I have ever seen before.
You're also missing the point of most of the arguments. Short of the fact that Night of the Comet is hardly the epic it used to be, flawing your argument, the argument isn't that you can't survive, the argument is that the skill tree effectively leads you to specialize in either ship or a BO class, and even in certain builds, while effectively punishing you for trying other builds (because of supporting skill cost) or for trying to balance out your character.
Also, Night of the Comet, even in its toned down form, is still a PvE regular mission environment. There are no timers in it, and no PLAYER fighting you. With those restrictions I can easily make something survive even the harder version of it. Lets be honest, you don't need BO skills in missions. You don't need weapon damage in missions, or super survivability. Mobs are by definition stupid. Its not hard for (most) players to out think them. Any weakness in your build is ignored by the Mobs, and generally most players can play to their strengths.
On the other hand, STFs have time limits, and much harder mobs. PvP is against other players that think and adapt. Any weakness in your build will either gimp the team in STFs (especially in Elite versions) or in PvP be ruthlessly exploited, causing cries of foul, noob, and this game sucks, to echo across zone chat.
Also, as I mentioned I can very easily build around certain builds and cry: see my build works, this is GREAT. Now go make a decent survivable build for PvP based around Scramble Sensors, Cloaking, and Viral Matrix that does any kind of decent damage. (Yes I know there are various arguements for and against using those skills in PvP... its not the point). Now build one around Tractor Beam and Gravity Well? That Gravity Well Build was much easier wasn't it?