How come only games for Nintendo systems seem to suffer from this case of "not enough to go around" as you put it?
From my understanding, cartridge based games (GBA and DS in modern terms) are much more expensive to produce per item relative to CD/DVD ones (GameCube/Xbox, etc.). The profit per item is also much lower. You aren't going to want to make millions of them if you aren't sure they're going to sell. I assume GameCube games are just as easy to find as other CD/DVD based systems. If I make $20 profit from one DS game sold, I can manufacture 2 more copies. Yet if I make $50 profit from one Xbox game sold, that's enough to pay for 5 more copies.
I own a PS1, PS2, XBOX and dreamcast and I never had much problems finding any of the titles that I wanted.
Optical-based systems. Even then, there are rare games for these systems. Suikoden 2 for PS1 gets around $100 on eBay. Valkyrie Profile PS1 gets that much occasionally (although its price might be affected by the PSP release). For a while, Final Fantasy Tactics PS1 was the same before its Greatest Hits reprint (an honor reserved for games selling a certain amount that FFT didn't actually sell). On PS2, Rez was/is hard to find. On Dreamcast, Marvel vs. Capcom 2 goes for $50 plus on eBay. I don't know the pricing for it, but Panzer Dragoon Orta on Xbox is a very well received game that's impossible to find outside of eBay even a single year after it came out. Marvel vs. Capcom 2 on Xbox is also a rare find. Notice these are all fairly niche titles that do not warrant producing excessive copies. Even Squaresoft didn't gamble on FFT on its initial run, and only reprinted it as a GH after the Final Fantasy brand became very well known.
You can find Trauma Center and other rarer DS/GBA games on eBay quite easily, you'll just pay more than the MSRP for them.
Bottom line is, I shouldn't have to go to ebay to find a pretty popular game for a system that is less than 2 years in the market. As a comparison I can still find or order online all the popular games, brand new, for the Xbox, which has been far longer on the market than the DS.
But it isn't a pretty popular game. My definition of popular is a game that will definitely sell well to the average consumer, not to a niche market as Trauma Center and Phoenix Wright both certainly are. Both these games have virtually no marketing and are aimed towards the hard core gamer market, which is very small compared to the Super Mario one. This is proven by the fact that Trauma Center still sits unsold on shelves in several parts of the country as people have commented in this thread. It's also why several online retailers have dropped Trauma Center (new, not used) from its online catalogue, yet the game is still available for purchase from Atlus directly.
I don't know - I'm basically a PC gamer, so I'm not used to this either.
PC games are very different to console ones. PC developers do not have to pay licensing costs to Microsoft to develop games for Windows. At least I know they didn't before, I don't know about now. Even so, console developers also have to pay for development kits which I think cost around $10,000 to $20,000 per kit. Unlike licensed PC software tools or engines, console development kits come with hardware (developer versions of the consoles themselves) that can't be duplicated to use on several machines. Additionally, anyone can print their own CDs for PC games, while on consoles they can't. Nintendo gets paid to make the cartridges for other publishers. When someone publishes a game, they're paying Nintendo to make them, Sony to print game DVDs for them, etc. On CD/DVD based consoles, this comes out to about $8-10 profit for the console maker per item manufactured. These costs increase even more when going to cartridge due to production differences. The fact DS and GBA are cheaper compared to console games means the profit per item is much less, making it less of an incentive to make more cartridges. Why pay more money to make less profit per item?
As a caveat, I might be wrong about some of these facts.
Is this wacky Japanese export title/anime genre unique to Nintendo titles as opposed to other console systems? If so, that could be why. The companies that make them perhaps aren't interested in producing that many for the USA.
No, it isn't unique at all. Games like Disgaea on PS2 were never reprinted and are in short supply but are fan favorites (yet not popular) are niche games. Panzer Dragoon Orta is an Xbox example. The fact you call it "wacky" shows it really isn't mainstream, so it doesn't warrant producing many units. Nintendo will collect fees no matter how many are sold, so no company is going to risk producing an excessive amount. This is also why Nintendo games are usually easier to find even if they don't sell well (but not always).
Console makers make little, no, or lose money per console sold. They make all the money on licensing fees, which they don't have to pay if they are publishing titles for their own console. This is why they all want their own consoles. Sega, Nintendo, NEC, SNK, Atari, etc.