You brought up NIS/Atlus as good games to pre-order, and other rarities... I would also offer that games that I *want* to support, games that I *demand* be recognized should be pre-ordered (just like movies that I like I *want* to add to the box-office numbers, even though I fucking *hate* the theater). Re-releases are the best example of this (FFX/2HD, and Tactics Ogre (PSP) come to mind, the latter also rewarding that loyalty with a neat deck of Greater Arcana), but SSB4 giving me the "for fun/for glory" bit puts that on my pre-order list as well (Granted, I can't see them DLCing themselves into getting fucked with SSB, one of their big series, so I'm not too worried that I'm supporting shit practices).
Squaresoft isn't a terrible example of it *working*, either. Look at how Squeenix reacted to Bravely Default and FFX selling and being pre-ordered in the quantity they were, going to far as to issue an apology and, while it remains to be seen (I'm just hopeful, and screw it, there's little enough to be hopeful about otherwise), possibly changing their focus as a business.
So there are three ways I can enjoy a game... I pre-order it if I support its ideas, its company, or similar. Also, usually the pre-order gives me something (though this is becoming drastically less common). According to my pre-order history, the last three games I pre-ordered were FFX, Dragon's Crown, and Tactics Ogre: Let Us Cling Together, so grain of salt (I'm sure that's not all of it, that's just my card). I can buy it at retail, usually if it's a game I'm tenuous of, and it gets good reviews (Deus Ex: Human Revolution, offhand). Or I can wait for a used, borrowed, etc. copy if it's that I want to experience it, and then I'll usually snag something else by them, new, if it's good (Which is how I got into NIS/Atlus, with Disgaea for six bucks years ago).
People need to be discerning when they buy games, in order to improve the industry, and most people don't take gaming seriously enough to do so. Just like MovieBob noted about Bay: You can't really blame him for selling to the least-common-denominator if that's who's actively buying the shit. We just need companies committed to decent games, and to support them as much as we can. It's a little hard to sort one pile of shit from another (N seems to be about the only candidate for that I can offer without addendum), but this is why I think people should know their gaming histories.
There are fanboys and pedigrees to consider, and kickstarter stands on the other end of this chain (I shamelessly backed Unsung Story/Mighty No. 9, so I'm *willing* to pre-order a game before it's even made, but in this case it's made by people who have a creation history where I've loved every game they made...). There's capability for abuse and bullshit, but, on the other hand, it's not all negative as a concept, it's just heavily abused by fucktards, and too many people let themselves be abused instead of being better *customers*.
EA, Ubi, SEGA (excluding a couple of their teams, perhaps) have solid histories of bullshit, and yeah, probably shouldn't be given the benefit of the doubt... Squeenix I'm on the fence about, but they seem like they finally get it... N? Them I'll toss money at hand-over-fist... Re-releases of awesome games? Games with feelies as pre-order bonuses? Yeah, yeah I can do that.