Polish needs to be a category. aka the reason Suikoden 5 isn't whoamfg best game ever (well that and gameplay I guess <_<).
The categories VSM originally has pretty much cover everything, so viciously dissect them until we find out what makes them tick!
Regarding Polish and Overall categories, I think it would be useful to take these apart and probably relegate them to sub-categories in other areas.
Polish in gameplay, Polish in menus (FFT's menu options are very useful, but actual menu composition? not fantastic, especially the obscure location of the who-moves-when list) and systems (think the difference between FFX growth and Rogue Galaxy growth).
For Overall, what games are more than the sum of their parts, and why? the invisible web that makes them that way can be discerned into individual threads of synergy between discrete categories, I think.
Take Suikoden 2. It has major deficiencies, but is generally very well thought of. I think it's fair to say the game is better than it might objectively rank if you gave it a 1-10 in each major category. Here are some preliminary thoughts as to why:
#1 Immersive plot. What I mean by immersive is, it has emotional hooks that extend into other areas. The game's music, in a vacuum, is not incredible as a whole, I think, but it works very, very well ingame. Plot and music synergistically improve one another.
Plot, to my eye, deserves subcategories, particularly to separate plotline writing from diologue, and also to reward good directing (something that comes out both in visuals and sound as well, of course)
#2 Speedy Combat. Combat in the game is simple (other than a few neat conceptual ideas with some runes) and, befitting simple combat, it's freaking fast. You can conclude an S2 random encounter by the time you might in another game be inputting your first action. It's easy to undervalue combat that is dull on paper, but the pacing makes it inoffensive at worst, at least until you slow down to think about it. WA1 is, to me, the diametric opposite. Combat should be interesting, and it certainly is on paper, but random encounters are sloooooow and dull in practice.
Should combat facility possibly be counted separately from combat system quality?
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One other thing that's worth considering is things that make games baaaaaaaad. Unforced errors, I'd call them. Things for which there is no excuse. Don't think they should be their own category, but looking at them may sharpen our ideas of what constitutes good.
Here are some off the top of my head:
Suikoden 2 - Making you use Freed Y. - TWICE (ok, not a huge deal, but still...)
Suikoden 4 - Sailing, natch.
Star Ocean 3 - IC. maybe not by itself, but compared to SO2 it's such a step down that it's kinda incomprehensible why it turned out so badly.
Dark Cloud - Swords that break like they're flourescent lights.