Honestly, Nature does mean something. It increase one stat by 10% and decreases one by 10%. 10% of a stat is a lot. In the end Nature is one of the most important aspects of a Pokemon.
Since you Rayquaza is mild, therefore it increase Sp. Attack the poster above me has a pretty good set...
I use my Masterballs on everything. Cloning is your friend in 3rd Gen/4th Gen. In the 1st Gen I accidentally used mine on a Weezing...Gold/Silver I always waited for the legendaries.
Gyarados in Silver, which should be all of your first shinys if you owned gold/silver. Still have neglected to capture a 3rd/4th Gen shiny but really what does it really matter if the COLOR is different. I personally don't give a crap but that's just me.
IDK the 3rd Gen unfortunately I have to say was my least favorite. I thought that it was incredibly easy I didn't 'black out' once. Emerald gave us the Battle Frontier but not much else. The only thing spectacular about this Gen IMO was the graphics. An incredible step up from G/S/C and not much...
My Secret Base.
Definitely the easiest and least time consuming method IMHO. I just switch out the Pokemon when I need a different Ev to be trained it. Plus all my Pokemon only have one non-attacking move that I use for my Secret Base. Therefore there is no harm for my Pokemon that I want to be...
That was an eye-opening statistic. I agree 100% that Pokemon should be more balance as far as types go. The only thing that is under numbered that we don't need are a bunch of new dragons, each is unforgettable and will always be known as a powerhouse.
Even if the GTS is broken and there are many stupid people, you can still find diamonds in the rough. I have gotten numerous amazing things from the GTS. You just have to look harder for the best deals.
Yes, even though "nothing lasts forever" I'll give my kids all my games along with my extensive card collection that will hopefully be worth something someday.