After spending way too much time keeping my name set complete and getting update packs for each version I started using a simpler approach so I spend more time playing MAME than updating it.
This method relies on romset names being fairly stable and I'm using a non-merged set and bios included in rom sets. (I include them so BIOSes don't show up when I'm running MAME directly)
Like Denzilla, I did the one time approach of manually removing all games I did not want. Even if it was non-working, or my current machine wasn't powerful enough, I included the rom set, so in the future I would have it. Since I used non-merged set, I could be selective on exact version of roms I wanted. (For example, the world version of Double Dragon, ddragonw, not ddragon)
Once I had my roms slimmed down, I use a simple BASH command (OS X) or PowerShell command (Windows) to list the rom directory without the extensions) into a text file. So now I have a text file with just the roms I want. (Called Favourites.txt in my case)
When a new version of mame comes out, I add it ClrMamePro. I go to the Scanner and Click the Set Info button. In this screen there is an option to load a text file, which we supply the text file created earlier. (Favourites.txt) This will cause only the roms I want to be included. ClrMamePro takes care of the individual roms in each rom set, I don't have to worry if a specific rom was added or deleted with, because I am just filtering by rom set name. It's almost instant, and I can than save a dat from the same window and use this in ClrMamePro.
With this my rom set is so much smaller and updating in fairly painless. Every once and a while new files my be added in newer mame versions to game I have, but it is simple to see what I need and a lot easier to find on the internet than getting entire update packs, which are generally 99% for games I don't want.
On my PC I have mame version 0.202, but on my Raspberry PI 3, it's only using MAME_2003plus which uses a mame 0.78 romset.
No problem, load dat file for mame 0.78 into ClrMamePro, read my favourites.txt file, I can now save a dat for just the games I want that only play with that version of MAME. If your favourites text file has game that was added in a later version of mame, it is simply ignored. ClrMamePro does all the work of selecting the right specific roms for the rom set you want, for that version of mame.