@robot#2, I have i5-4690 3.5GHz, 8Gb RAM, GPU GTX550Ti 1024 Mb.
With SVE 1.1.6 LR, bundled Scatterer 0.0300 , RealPlume, RPM+ASET cockpit and many other mods that shouldn't affect FPS much I had 9-10 FPS at the runway. Although, it's not necessary the visual mods who eat FPS as mods that perform some hard calculations or suboptimal seeks may also reduce frame rate significantly, as well as heavy log spam does, so they worth checking too.
Here's what I've done:
Updated video driver (but that not necessarily would increase or even save your FPS at current value)
Run KSP with -force-d3d11.
Disabled Godrays, terrain shadows, accurate sky reflections in Scatterer. Also I have ocean Fourier grid size set to 64 (32 makes it look too weird).
While in Flight scene I pressed Alt-0 to bring up EVE config. Navigated to clouds page and removed the Layer volume for Polar snow. That gave me +4 FPS instantly, despite of the fact that the snow wasn't ever visible.
But the worst evil for us are volumetric clouds, unfortunately. Decreasing the "distance" value according to SVE's author recommendations to 4000, 2000, 1000 hadn't brought much difference. So I just disabled all the Layer volumes.
Having all that done I have 17, sometimes 20 FPS at the runway. At least KSP clock isn't yellow all the time now . At the title screen I have 60 FPS. But sometimes when I run KSP I see FPS settled at the value of 45 at the title screen for some reason and 10-14 at the runway. Restarting the game brings back normal numbers, so pay attention to that too.
Another factor I've noticed is software that runs in parallel. Having Firefox with KSP forums and Spacedock open I've noticed that my monitoring software showed 30% GPU load . Not sure, may be that was 30% of 50MHz to which my GPU slows down when not doing graphically intensive tasks but it's better to run the game with the number of software working in parallel minimized.
Also I've spent a weekend baking pancakes on my GPU (i.e overclocking it) and got +15% performance out of it. As a result other graphically intensive games have got +4-5 FPS but there's no effect in KSP (I won't tell that FPS even seem to be slightly reduced as I refuse to believe it).
And I've tried [1.2] Para-Sci High-Performance Atmosphere Pack v1.1 recommended in SVE's OP for laptops but had even worse frame rate, so that's all I've managed to get out of my system to the moment.
You do not need to worry. This is how MiniAVC (the version checker used by some mods) works: it looks at the version of KSP that modder has typed as compatible for his mod and if it differs from the current KSP version it starts to yell. But that not necessarily means that mod doesn't work with that version, it's just about the mod's metadata getting obsolete with a new KSP version installed. Some mods have yelled during two or three KSP versions and worked fine, so unless you have real troubles that's not an issue.
