actually with the silver case and especially skullgirls they seem to be testing the waters for a pre-order market, they also stated that although they give the developers a number they think will sell its ultimately up to the developer not LRG to select a quantity to produce.
also you need to seriously keep in mind that most/all of these games are indie games with very low fandoms and if they didn't sell them in a limited quantity like they do then there would be no guarantee that they would even sell as many copies of these games as they produce.
A good point, but a huge reason why people want to buy these games isn't necessarily because they're fans of the games: people like physical copies of stuff, even though they don't have an interest in actually playing the game. And the allure of a rare and limited release also makes even more attractive for collectors, even if the game itself has a low following.
Firstly, LRG has specifically stated they will not print a second batch of
any game they release, so they still purposefully limit availability of their titles, no matter how popular the are. Secondly, when talking to developers, LRG finances the entire project themselves, so they actually do have the ultimate say in how many copies they would like to make. But I think it's good that they're stepping up the production numbers and trying out a pre-order system.
Some examples to address to your second point:
Oddworld is not really a franchise with a low number of fans, it's a relatively popular and well known series.
They want to publish Phantasy Star Online 2, and have expressed interest in Fatal Frame V: games that also have followings and fanbases
and...
Breach & Clear was the number 1 strategy game in 40 different countries on it's original platform (iOs), and was the number 2 game in 2013 in the United States.
In addition, my issue still stands: If at any point in the future you want to own any of these game for
any reason, it will be next to impossible and frustratingly expensive (as it stands right now).
What if you want to collect for the PS4? Or the Vita?
What if you hear about Octodad in a YouTube video and want to try the game out?
What if you played Shantae on the 3DS and want to check out some other games in the series?
You would completely miss out because you were late to the party
Again, we don't like how other rare games are like that now, I'm not thrilled that LRG is making releases that play into that same situation, whether it makes sense from a business perspective or not.