Emulator

Game Name? Super Mario Galaxy 1

Game ID? RMGK01

What's the problem? Describe what went wrong in few words.
SMG1 runs on IR 1x and LLE mostly at 60fps, but certain demanding areas cause the FPS to drop to 45-55, and gameplay is affected (and sound stutters even worse). This is expected on my hardware.
Frame Skipping option set to 1 causes (on my computer, with ok i5-4670S and bottlenecingly underpowered Intel Hd 4600) FPS to drop to 30 without affecting actual game speed (as the feature should work), it runs responsively, video playback is somewhat "less smooth", but playability remains near perfect.
Frame skipping won't work on all games and I don't want to turn it on all the time. (At the moment, the option isn't saved at all, resets to 0 after Dolphin restart).

What did you expect to happen instead?
I'd be able to define Frame Skipping in gameini (for example [Video_Hacks] FrameSkipping = [0-9]), only to be used in games that benefit from it.

What steps will reproduce the problem?
See above. Restarting Dolphin erases the selected Frame Skipping value, and playing a different game requires to manually turn it off.
[Don't assume we have ever played the game and know any level names. Be as
specific as possible.]
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Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
4.0.624 (tev_fixes_new) x64, seems to be in older master builds also.

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
Frame skipping GUI hasn't been altered since don't know when.

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
Win 8.1 x64, i5-4670S, Intel HD 4600.

Are you using the 32 or the 64 bit version of Dolphin?
64-bit

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
No.