Lately I've been comparing the performance of some versions of Dolphin. I noticed that the emulation of the Gamecube was much more fluid in version 5.0 (stable) and running the games without any lag, but the emulation of the Wii was considerably slower. Now in the latest (development / daily) versions I can not emulate a Gamecube game satisfactorily, it always gives lag and stutters in most games, while Wii emulation is much better compared to the 5.0 stable version.
A good example is Metal Gear Solid - Twin Snakes. In the current versions the game runs perfectly, until the enemies are alerted and begin to attack, then the game begins to lag. This does not happen in previous versions, it's normal?
Yes. GPU requirements rised since 5.0 because accuracy is even better now (ie XFB have a proper implementation and always On now).
However, you have a powerfull GPU, I guess you're experimenting shader stuttering. Try Asynchronous Shader Compilation (UberShaders) that negates this effect. Also, try switching between Video Backends until finding the best one for your GPU/game combo.
Mixture of XFB2RAM + Slower MMU is what makes MGS more demanding. Still, an i5-7400 should be more than enough. On dualcore, my i5-3570K could easily maintain full speed in it.
The other option is always to run multiple versions of the emulator. Maybe this comes from the fact that I went through the early days of 16 bit and 32 bit emulation, but Dolphin takes very little space as a program that having a version that might be less accurate overall but works great on some subset of games is not a horrible idea.
I remember for the PS1 having multiple different emulators and multiple different versions of those emulator to get certain games to work. Xenogears and Chrono Cross both required at points in the life of ps1 emulation to be not only plyed across diferent versions to work but for the saves to be converted and some parts to be played on different emulators to complete those games. There were others but these came to mind. (Funnily enough Xenogears had a game breaking crash with the official emulator on the PSP as well durring the Deus fight if not handled properly)
Even with ubershaders this happens. The components of my pc in general do not even reach 30% of use during the game. I'm sure it's a problem of the emulator itself.
Something's definitely going above 30% load, although it might not be obvious what. For example, if you're CPU bottlenecked, you'll see 30% CPU usage spread across all cores, but that's just because your OS is switching Dolphin between multiple cores to evenly distribute heat and Dolphin is using 100% of the two cores it's actually using.
Honestly you haven't shown us your full specs or your settings so we're all speculating.