Oh, I completely agree Idle. When I slapped it together originally (and when The_Butt followed it up with his update), MSE2 wasn't capable of making anything less than a hack pokemon template (too many non-uniform elements to really work with at the time.) Now that MSE2 is further along I'm sure a much, much better template could be put together. As far as the game file goes, tear apart, start over, do whatever you like. There's a lot of user following to this template, but pretty much everyone that has ever voiced an opinion on it has voiced that they would prefer having the newest pokemon card style available, so I doubt there would be too much upset over it. One thing you could do is create some reverse compatibility scripts. I did it a couple years ago when VS got a huge overhaul that made old sets unreadable. Basically I just added some script that would default old fields and choices that would appear in set files but not the game or style files to new fields and choices that would. So, in the case of of a trainer card, it might go something like:
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old_to_new := { if card.card_type=="trainer" then "colorless" else card.card_type(value) }
And I honestly have no idea if that script would work correctly, I'm tired after work but it gives a general presentation of what I'm talking about.
Good luck with everything, and don't worry about breaking things. It was a hack job to begin with, and what everyone really wants are the new styles anyways.