Let's look at it two different ways.
Pretend you go to McDonald's and eat a Big Mac three times a week for the whole year. Then, at the end of the year, they start running the Monopoly promotion. Do you go to the counter and complain that McDonald's owes you Monopoly coupons for the whole year's worth of Big Macs you ate that didn't come with coupons?
Second, let's say that, tomorrow, Nintendo of America was to issue a press release that stated, due to the declining economy, Nintendo is forced to raise their MSRP of all games by $10... making most GBA/DS games $40-$45 and most GCN/Wii games $60...
...Should you have to go back through all your previous purchases, figure up the difference between the new price and the old price and cut Nintendo a check for the newer prices? (Damn, I hope not or I'm screwed...)
The Club Nintendo offer was not taking place when you purchased the older titles. You never should have expected anything more from purchasing the game than the game you got. It's not Nintendo's fault you had extra expectations of what you felt you deserve.
Frankly, the way they are doing it right now, it's almost as if they aren't doing it at all. Limit the number of games a person has registered to count under the new rules. I registered Metroid Prime 2 and Super Mario 64 DS only a few days apart, but only SM 64 DS counts. No Gameboy Advance, no Gamecube games allowed!
Let's be honest, MyNintendo was never a rewards program, it was a market research program with minimal effort by Nintendo. Put up a website/programs, print up some codes and put with games and let them do the work for them.
I would *almost* agree with the way some DS/Wii games count and some don't. But it's quite simple that the GBA/GCN is dead - the few games that are still out there, Nintendo's not really going to see a profit from, so they have no reason to encourage their sales.
MyNintendo wasn't *much* of a rewards program, you're right. Although I do like some of the various physical prizes I've received - I never downloaded any of the free virtual gifts. But, the point is, Nintendo could have kept the MyNintendo program going... they're doing something extra here (Again, keeping in mind that Wallpapers and such was a good chunk of the Euro-Club Nintendo). It's free and if you don't like it, you don't have to participate. Send me your codes and I'll take the free stuff.